smartdenovo make error

[Bearmax90]

$make gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o pairaln file_reader.c ksw.c pairaln.c -lm -lpthread gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtpre file_reader.c wtpre.c -lm -lpthread gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtcyc file_reader.c ksw.c wtcyc.c -lm -lpthread gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtmer file_reader.c wtmer.c -lm -lpthread gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtzmo file_reader.c ksw.c wtzmo.c -lm -lpthread gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtobt file_reader.c wtobt.c -lm -lpthread gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtclp file_reader.c wtclp.c -lm -lpthread 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/cc6478e6.o: In function merge_bubbles_strgraph': wtlay.c:(.text+0x984d): undefined reference tocut_biedge_strgraph2' wtlay.c:(.text+0x9861): undefined reference to cut_biedge_strgraph2' wtlay.c:(.text+0x992d): undefined reference tocut_biedge_strgraph2' wtlay.c:(.text+0x994a): undefined reference to `cut_biedge_strgraph2' collect2: error: ld returned 1 exit status Makefile:48: recipe for target 'wtlay' failed make: *** [wtlay] Error 1

PS information: $gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.5.0-3ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)

$cpp -v Using built-in specs. COLLECT_GCC=cpp OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.5.0-3ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04) COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/7/cc1 -E -quiet -v -imultiarch x86_64-linux-gnu - -mtune=generic -march=x86-64 -fstack-protector-strong -Wformat -Wformat-security ignoring nonexistent directory "/scratch/bin/samtools/include/" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/7/../../../../x86_64-linux-gnu/include"

include "..." search starts here:

include <...> search starts here:

/usr/lib/gcc/x86_64-linux-gnu/7/include /usr/local/include /usr/lib/gcc/x86_64-linux-gnu/7/include-fixed /usr/include/x86_64-linux-gnu /usr/include End of search list.

[Bearmax90]

I hope to get your help. Thank you very much.

[Bearmax90]

I successfully installed Smartdenove with Conda built from my user directory. However, I still can't make it from its setup package using 'make'. Under these conditions, I ran the 'smartdenove.pl' program with no result.

$cat sont.mak PREFIX=sont

EXE_PRE=/home/u3798/anaconda3/bin/wtpre EXE_ZMO=/home/u3798/anaconda3/bin/wtzmo EXE_OBT=/home/u3798/anaconda3/bin/wtobt EXE_GBO=/home/u3798/anaconda3/bin/wtgbo EXE_CLP=/home/u3798/anaconda3/bin/wtclp EXE_LAY=/home/u3798/anaconda3/bin/wtlay EXE_CNS=/home/u3798/anaconda3/bin/wtcns N_THREADS=12

all:$(PREFIX).dmo.cns

$(PREFIX).fa.gz: $(EXE_PRE) -J 5000 ../ont.fastq | gzip -c -1 > $@

$(PREFIX).dmo.ovl:$(PREFIX).fa.gz $(EXE_ZMO) -t $(N_THREADS) -i $(PREFIX).fa.gz -fo $@ -k 16 -z 10 -Z 16 -U -1 -m 0.1 -A 1000

$(PREFIX).dmo.obt:$(PREFIX).fa.gz $(PREFIX).dmo.ovl $(EXE_CLP) -i $(PREFIX).dmo.ovl -fo $@ -d 3 -k 300 -m 0.1 -FT

$(PREFIX).dmo.lay:$(PREFIX).fa.gz $(PREFIX).dmo.obt $(PREFIX).dmo.ovl $(EXE_LAY) -i $(PREFIX).fa.gz -b $(PREFIX).dmo.obt -j $(PREFIX).dmo.ovl -fo $(PREFIX).dmo.lay -w 300 -s 200 -m 0.1 -r 0.95 -c 1

$(PREFIX).dmo.cns:$(PREFIX).dmo.lay $(EXE_CNS) -t $(N_THREADS) $< > $@ 2> $@.log

[ruanjue]

What happened when execute make sont.mak ?

[Bearmax90]

What happened when execute make sont.mak ?

make: Nothing to be done for 'sont.mak'.

[Bearmax90]

I reinstalled the software manually, according to #18. Then, the 'smartdenove.pl' workd. Anyway, thanks again.