Fatal error when installing aracon

[shilaixing]

Hello! I tried to install aracon on my Linux service (CentOS release 6.2) with following steps： 1) git clone https://github.com/isovic/aracon.git 2) cd aracon 3) make

The installing process was stoped with the following messages: [GET MODULES] Submodule 'components/graphmap' () registered for path 'components/graphmap' Submodule 'components/miniasm' () registered for path 'components/miniasm' Submodule 'components/racon' () registered for path 'components/racon' Submodule 'components/samscripts' () registered for path 'components/samscripts' Submodule path 'components/graphmap': checked out '1d16f07888b60547094e8257688088d6f00be8af' Submodule 'codebase/argumentparser' (https://github.com/isovic/graphmap.git) registered for path 'codebase/argumentparser' Submodule 'codebase/seqlib' (https://github.com/isovic/graphmap.git) registered for path 'codebase/seqlib' Submodule path 'codebase/argumentparser': checked out 'd0dae52c3d1b029f65f3bf4f0cd671e88dbeb98f' Submodule path 'codebase/seqlib': checked out 'e0833dc91343ac7a1e33fb6b2f08bc9009bf9a8b' Submodule path 'components/racon': checked out '0bb2fd6ca9fa4492b0ba7b6751d242795c02f6fa' Submodule 'codebase/argparser' (https://github.com/isovic/racon.git) registered for path 'codebase/argparser' Submodule 'codebase/samscripts' (https://github.com/isovic/racon.git) registered for path 'codebase/samscripts' Submodule 'codebase/seqlib' (https://github.com/isovic/racon.git) registered for path 'codebase/seqlib' Submodule 'codebase/spoa' (https://github.com/isovic/racon.git) registered for path 'codebase/spoa' Submodule path 'components/samscripts': checked out 'b40d0663f6a5c477d5f6908f83567758fb627e08' Entering 'components/graphmap' From https://github.com/isovic/graphmap

• branch master -> FETCH_HEAD Updating 1d16f07..817ba03 Fast-forward Makefile | 2 +- README.md | 6 +- codebase/argumentparser | 2 +- codebase/seqlib | 2 +- doc/changelog.md | 6 ++ src/alignment/anchored.cc | 2 +- src/alignment/cigargen.cc | 146 +++++++++++++++++++++++++++----------- src/alignment/cigargen.h | 20 ++++++ src/graphmap/graphmap.cc | 6 +- src/graphmap/graphmap.h | 7 ++ src/graphmap/process_read.cc | 2 +- src/graphmap/region_selection.cc | 19 +++-- src/index/index.h | 67 +---------------- src/index/index_hash.cc | 10 ++- src/program_parameters.cc | 9 +-- src/program_parameters.h | 3 +- 16 files changed, 176 insertions(+), 133 deletions(-) Entering 'components/miniasm' From https://github.com/lh3/miniasm
• branch master -> FETCH_HEAD Already up-to-date. Entering 'components/racon' From https://github.com/isovic/racon
• branch master -> FETCH_HEAD Updating 0bb2fd6..bd1a7c1 Fast-forward .gitignore | 1 + Makefile | 3 +- README.md | 65 ++++- codebase/argparser | 2 +- codebase/samscripts | 2 +- codebase/seqlib | 2 +- example1-lambda.sh | 56 ---- example11-erc-ecoli_map006.sh | 155 ----------- ...ple12-paf-lambda.sh => example1_1-paf-lambda.sh | 5 +- ...le7-mhap-lambda.sh => example1_2-mhap-lambda.sh | 6 +- ...hap-ecoli_map006.sh => example1_3-sam-lambda.sh | 53 ++-- example2-paf-pipe-lambda.sh | 102 +++++++ example10-erc-lambda.sh => example3-erc-lambda.sh | 7 +- example8_1-mhap-ecoli_map006-1111.sh | 122 -------- example8_2-mhap-ecoli_map006-pileup.sh | 122 -------- example9-mhap-ecoli_pacbio_160x.sh | 122 -------- example9_1-mhap-ecoli_pacbio_160x-1111.sh | 122 -------- run-measure.sh | 13 - scripts/edcontigs.py | 2 +- scripts/evalcontigs.py | 2 +- scripts/intervaltree.py | 2 +- scripts/lis.py | 2 +- src/consensus/consensus.cc | 195 ++++++++++++- src/consensus/consensus.h | 6 +- src/consensus/pileup.cc | 2 +- src/consensus/pileup.h | 2 +- src/main.cc | 205 ++++++++------ src/mhap.cc | 290 +++++++++++++------- src/mhap.h | 20 +- 29 files changed, 727 insertions(+), 961 deletions(-) delete mode 100755 example1-lambda.sh delete mode 100755 example11-erc-ecoli_map006.sh rename example12-paf-lambda.sh => example1_1-paf-lambda.sh (98%) rename example7-mhap-lambda.sh => example1_2-mhap-lambda.sh (95%) rename example8-mhap-ecoli_map006.sh => example1_3-sam-lambda.sh (74%) create mode 100755 example2-paf-pipe-lambda.sh rename example10-erc-lambda.sh => example3-erc-lambda.sh (95%) delete mode 100755 example8_1-mhap-ecoli_map006-1111.sh delete mode 100755 example8_2-mhap-ecoli_map006-pileup.sh delete mode 100755 example9-mhap-ecoli_pacbio_160x.sh delete mode 100755 example9_1-mhap-ecoli_pacbio_160x-1111.sh delete mode 100755 run-measure.sh Entering 'components/samscripts' From https://github.com/isovic/samscripts
• branch master -> FETCH_HEAD Updating b40d066..8225661 Fast-forward src/alignmentstats.py | 2 +- src/apply-consensus.py | 2 +- src/consensus.py | 2 +- src/count_mapped_reads.py | 2 +- src/errorrates.py | 2 +- src/fastqfilter.py | 4 +- src/fastqparser.py | 2 +- src/samfilter.py | 2 +- src/svconsensus.py | 2 +- src/utility_sam.py | 515 ++++++++++++++++++++++++++++++++------------- src/vcffilter.py | 2 +- src/venn_of_sams.py | 2 +- 12 files changed, 385 insertions(+), 154 deletions(-) [GraphMap] components/graphmap/bin/Linux-x64/graphmap cd components/graphmap; make modules && make -j 4 make[1]: Entering directory `/share/work2/staff/xingsk/software_install/Minisam_Racon/aracon/components/graphmap' git submodule update --init --recursive Submodule 'codebase/argumentparser' () registered for path 'codebase/argumentparser' Submodule 'codebase/seqlib' () registered for path 'codebase/seqlib' Submodule path 'codebase/argumentparser': checked out '72af9764acefbcc92ff76e3aba8a83d9a3e33671' Submodule path 'codebase/seqlib': checked out '129d39a97ba56863bea98d3125f4241b26f36341' git submodule foreach git pull origin master Entering 'codebase/argumentparser' From https://github.com/isovic/argumentparser
• branch master -> FETCH_HEAD Already up-to-date. Entering 'codebase/seqlib' From https://github.com/isovic/seqlib
• branch master -> FETCH_HEAD Updating 129d39a..a93e7d9 Fast-forward src/utility/utility_general.cc | 8 ++++++-- src/utility/utility_general.h | 3 ++- 2 files changed, 8 insertions(+), 3 deletions(-) make[1]: Leaving directory /share/work2/staff/xingsk/software_install/Minisam_Racon/aracon/components/graphmap' make[1]: Entering directory/share/work2/staff/xingsk/software_install/Minisam_Racon/aracon/components/graphmap' Makefile:97: " WARNING g++ minor version <7 " mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/ g++ -static-libgcc -static-libstdc++ -Dcplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp mkdir -p obj_linux/codebase/seqlib/src/libs/ g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/edlib.o codebase/seqlib/src/libs/edlib.cpp mkdir -p obj_linux/codebase/seqlib/src/libs/ g++ -static-libgcc -static-libstdc++ -Dcplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/opal.o codebase/seqlib/src/libs/opal.cpp mkdir -p obj_linux/codebase/argumentparser/src/ codebase/seqlib/src/libs/edlib.cpp:4:19: Fatal error: cstdlib：No such file or directory compilation terminated make[1]: [obj_linux/codebase/seqlib/src/libs/edlib.o] error 1 make[1]: waiting for unfinished jobs.... g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/argumentparser/src/argparser.o codebase/argumentparser/src/argparser.cc In file included from codebase/argumentparser/src/argparser.cc:10:0: codebase/argumentparser/src/argparser.h:16:18: Fatal error：string：No such file or directory compilation terminated make[1]: [obj_linux/codebase/argumentparser/src/argparser.o] error 1 make[1]: No child processes. Stop. make: *** [components/graphmap/bin/Linux-x64/graphmap] error 2

So what can i do now?

[isovic]

Hi, Strange that the compiler cannot find the STL string header - which compiler (and version) are you using to make the project?

Best regards, Ivan.

[shilaixing]

The compiler version was gcc_5.4.0 (gcc >= 4.8). You remind me of the version, so I try another version(gcc_4.9.1). The good news is it works! Thank you very much!

[isovic]

Great, thanks! I need to inspect this in detail.

Best regards, Ivan.