Open AbRawoof opened 1 year ago
spoonbender76
commented
1 year ago make clean
Edit makefile. Add -no-pie in Line 58 and Line 62.
@$(CC) sparsePregraph/*.o standardPregraph/*.o -no-pie $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
@$(CC) sparsePregraph/*.o standardPregraph/*.o -no-pie $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
create a new conda env and install gcc9 by conda install -c conda-forge cxx-compiler=1.2.0 -y
make
kakadaisy
commented
11 months ago pregraph_sparse_63mer.v1.0.3 cleaning done.
/bin/sh: 1: g++: not found..
Error in command: g++ -c -O3 -fomit-frame-pointer -w -D63MER -m64 -I./inc build_graph.cpp
/bin/sh: 1: g++: not found.
Error in command: g++ -c -O3 -fomit-frame-pointer -w -D63MER -m64 -I./inc build_edge.cpp
/bin/sh: 1: g++: not foundp...
Error in command: g++ -c -O3 -fomit-frame-pointer -w -D63MER -m64 -I./inc multi_threads.cpp
/bin/sh: 1: g++: not found...
Error in command: g++ -c -O3 -fomit-frame-pointer -w -D63MER -m64 -I./inc build_preArc.cpp
/bin/sh: 1: g++: not foundcpp...
Error in command: g++ -c -O3 -fomit-frame-pointer -w -D63MER -m64 -I./inc pregraph_sparse.cpp
/bin/sh: 1: g++: not found
Error in command: g++ -c -O3 -fomit-frame-pointer -w -D63MER -m64 -I./inc io_func.cpp
/bin/sh: 1: g++: not found
Error in command: g++ -c -O3 -fomit-frame-pointer -w -D63MER -m64 -I./inc global.cpp
/bin/sh: 1: g++: not foundvo.cpp...
Error in command: g++ -c -O3 -fomit-frame-pointer -w -D63MER -m64 -I./inc convert_soapdenovo.cpp
pregraph_sparse_63mer.v1.0.3 objects generated.
/bin/sh: 1: gcc: not found
expr: 语法错误：未预期的参数 "4"
/bin/sh: 1: gcc: not found
expr: 语法错误：未预期的参数 "4"
SOAPdenovo-63mer cleaning done.
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc arc.c
/bin/sh: 1: gcc: not found.
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc attachPEinfo.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc bubble.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc check.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc compactEdge.c
/bin/sh: 1: gcc: not foundc...
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc concatenateEdge.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc connect.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc contig.c
/bin/sh: 1: gcc: not found...
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc cutTipPreGraph.c
/bin/sh: 1: gcc: not found.
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc cutTip_graph.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc darray.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc dfib.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc dfibHeap.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc fib.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc fibHeap.c
/bin/sh: 1: gcc: not found.
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc hashFunction.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc kmer.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc lib.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc loadGraph.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc loadPath.c
/bin/sh: 1: gcc: not found.
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc loadPreGraph.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc localAsm.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc main.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc map.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc mem_manager.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc newhash.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc node2edge.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc orderContig.c
/bin/sh: 1: gcc: not found..
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc output_contig.c
/bin/sh: 1: gcc: not foundc...
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc output_pregraph.c
/bin/sh: 1: gcc: not foundc...
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc output_scaffold.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc pregraph.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc prlHashCtg.c
/bin/sh: 1: gcc: not found.
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc prlHashReads.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc prlRead2Ctg.c
/bin/sh: 1: gcc: not found.
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc prlRead2path.c
/bin/sh: 1: gcc: not found...
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc prlReadFillGap.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc read2scaf.c
/bin/sh: 1: gcc: not found.
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc readInterval.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc stack.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc readseq1by1.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc scaffold.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc searchPath.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc seq.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc splitReps.c
/bin/sh: 1: gcc: not found..
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc cutTip_graph2.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc linearEdge.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc kmerhash.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc read2edge.c
/bin/sh: 1: gcc: not found
Error in command: gcc -c -O3 -fomit-frame-pointer -w -DMER63 -m64 -Iinc iterate.c
SOAPdenovo-63mer objects generated.
/bin/sh: 1: g++: not found
make: *** [Makefile:58：SOAPdenovo-63mer] 错误 127
############################################## Could anyone help in solving the installation issue?
supplement：I also successfully solved it using the above method from spoonbender67.
jomfer
commented
8 months ago
- make clean
- Edit makefile. Add
-no-piein Line 58 and Line 62.
@$(CC) sparsePregraph/*.o standardPregraph/*.o -no-pie $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer@$(CC) sparsePregraph/*.o standardPregraph/*.o -no-pie $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
- create a new conda env and install gcc9 by
conda install -c conda-forge cxx-compiler=1.2.0 -y- make
This solved the problem for me. Thanks a lot!
Hello I tried to install SOAPdenovo2 using the following in ubuntu (22.04.2 LTS) terminal $ git https://github.com/aquaskyline/SOAPdenovo2.git $ cd SOAPdenovo2
Then tried to install using make and make clean but got error related to multiple definition as shown below
SOAPdenovo2$ sudo make pregraph_sparse_63mer.v1.0.3 cleaning done.
pregraph_sparse_63mer.v1.0.3 objects generated.
SOAPdenovo-63mer cleaning done.
SOAPdenovo-63mer objects generated.
/usr/bin/ld: standardPregraph/attachPEinfo.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/bubble.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/check.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/compactEdge.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/concatenateEdge.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/connect.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/contig.o:(.bss+0x100): multiple definition ofshortrdsfile'; sparsePregraph/global.o:(.bss+0x1e0): first defined here /usr/bin/ld: standardPregraph/contig.o:(.bss+0x0): multiple definition ofgraphfile'; sparsePregraph/global.o:(.bss+0xe0): first defined here /usr/bin/ld: standardPregraph/contig.o:(.bss+0x200): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/cutTipPreGraph.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/cutTip_graph.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/cutTip_graph2.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/hashFunction.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/iterate.o:(.bss+0x48): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/kmer.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/kmerhash.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/lib.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/linearEdge.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/loadGraph.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/loadPath.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/loadPreGraph.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/localAsm.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/main.o:(.bss+0x32c): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/map.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/mem_manager.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/newhash.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/node2edge.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/orderContig.o:(.bss+0xc): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/output_contig.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/output_pregraph.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/output_scaffold.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/pregraph.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/prlHashCtg.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/prlHashReads.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/prlRead2Ctg.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/prlRead2path.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/prlReadFillGap.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/read2edge.o:(.bss+0x0): multiple definition oflocks'; sparsePregraph/global.o:(.bss+0x70): first defined here /usr/bin/ld: standardPregraph/read2edge.o:(.bss+0x40): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/read2scaf.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/readInterval.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/readseq1by1.o:(.bss+0x8): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/scaffold.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/searchPath.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/seq.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/splitReps.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: failed to set dynamic section sizes: bad value collect2: error: ld returned 1 exit status make: *** [Makefile:58: SOAPdenovo-63mer] Error 1#################################### Could anyone help in solving the installation issue.