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shendurelab / LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
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samtools-0.1.18 boost_1_52_0 #58

Open liyang16859 opened 5 years ago

liyang16859 commented 5 years ago

make[2]: Entering directory /export1/workdir/group1/liyang/software/LACHESIS-master/src' /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -static -lz -lpthread -Linclude -lJtime -lJgtools -lJmarkov -L/export1/workdir/group1/liyang/software/boost_1_52_0/lib -Wl,-R,/export1/workdir/group1/liyang/software/boost_1_52_0/lib -L/export1/workdir/group1/liyang/software/boost_1_52_0/lib -Wl,-R,/export1/workdir/group1/liyang/software/boost_1_52_0/lib -L/export1/workdir/group1/liyang/software/zlib-1.2.11/lib -L/export1/workdir/group1/liyang/software/bzip2-1.0.6/lib -L/export1/workdir/group1/liyang/software/xz-5.2.2/lib -L/export1/workdir/group1/liyang/software/pcre-8.41/lib -L/export1/workdir/group1/liyang/software/curl-7.47.1/lib -L/export1/workdir/group1/liyang/software/boost_1_52_0/stage/lib -L/export1/public/software/samtools-0.1.18/lib -lz -lpthread -lm -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -lboost_system -lboost_program_options -lboost_filesystem-mt -lbam -lz libtool: link: g++ -g -O2 -Wl,-R -Wl,/export1/workdir/group1/liyang/software/boost_1_52_0/lib -Wl,-R -Wl,/export1/workdir/group1/liyang/software/boost_1_52_0/lib -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -Linclude -lJtime -lJgtools -lJmarkov -L/export1/workdir/group1/liyang/software/boost_1_52_0/lib -L/export1/workdir/group1/liyang/software/zlib-1.2.11/lib -L/export1/workdir/group1/liyang/software/bzip2-1.0.6/lib -L/export1/workdir/group1/liyang/software/xz-5.2.2/lib -L/export1/workdir/group1/liyang/software/pcre-8.41/lib -L/export1/workdir/group1/liyang/software/curl-7.47.1/lib -L/export1/workdir/group1/liyang/software/boost_1_52_0/stage/lib -L/export1/public/software/samtools-0.1.18/lib -lpthread -lm -lboost_system -lboost_program_options -lboost_filesystem-mt -lbam -lz Lachesis-ChromLinkMatrix.o: In functionis_regular_file': /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference toboost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to `boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::NonDeNovoTrueMapping() const': /export1/workdir/group1/liyang/software/LACHESIS-master/src/GenomeLinkMatrix.cc:1062: undefined reference toHumanGenome_chroms()' /export1/workdir/group1/liyang/software/LACHESIS-master/src/GenomeLinkMatrix.cc:1063: undefined reference to HumanGenome_chrom_lengths()' Lachesis-GenomeLinkMatrix.o: In functionGenomeLinkMatrix::BinsPerChromInHumanGenome() const': /export1/workdir/group1/liyang/software/LACHESIS-master/src/GenomeLinkMatrix.cc:1558: undefined reference to HumanGenome_chroms()' /export1/workdir/group1/liyang/software/LACHESIS-master/src/GenomeLinkMatrix.cc:1559: undefined reference toHumanGenome_chrom_lengths()' Lachesis-GenomeLinkMatrix.o: In function is_regular_file': /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference toboost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to `boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference toboost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to `boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' Lachesis-GenomeLinkMatrix.o:/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: more undefined references to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' follow Lachesis-TrueMapping.o: In functionTrueMapping': /export1/workdir/group1/liyang/software/LACHESIS-master/src/TrueMapping.cc:128: undefined reference to HumanGenome_chroms()' /export1/workdir/group1/liyang/software/LACHESIS-master/src/TrueMapping.cc:134: undefined reference toHumanGenome_chrom_lengths()' /export1/workdir/group1/liyang/software/LACHESIS-master/src/TrueMapping.cc:136: undefined reference to HumanGenome_centromere_locs()' Lachesis-TrueMapping.o: In functionTrueMapping::TargetToHumanChromIDs() const': /export1/workdir/group1/liyang/software/LACHESIS-master/src/TrueMapping.cc:664: undefined reference to HumanGenome_chroms()' Lachesis-TrueMapping.o: In functionis_regular_file': /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' Lachesis-LinkSizeDistribution.o: In functionis_regular_file': /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference toboost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' Lachesis-ContigOrdering.o: In function is_regular_file': /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference toboost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' Lachesis-RunParams.o: In function is_regular_file': /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference toboost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' Lachesis-RunParams.o:/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: more undefined references to `boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code)' follow collect2: ld returned 1 exit status make[2]: [Lachesis] Error 1 make[2]: Leaving directory `/export1/workdir/group1/liyang/software/LACHESIS-master/src' make[1]: [all] Error 2 make[1]: Leaving directory `/export1/workdir/group1/liyang/software/LACHESIS-master/src' make: *** [all-recursive] Error 1

Huangtianyu-caas commented 3 years ago

Hi @liyang16859 ，

Did you fix this problem? I have faced the same issue.

My best, Tianyu