{"action":"created","issue":{"url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/39","repository_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2","labels_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/39/comments","events_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/39/events","html_url":"https://github.com/aquaskyline/SOAPdenovo2/issues/39","id":307624564,"number":39,"title":"Error during compilation","user":{"login":"michaelgruenstaeudl","id":7493028,"avatar_url":"https://avatars0.githubusercontent.com/u/7493028?v=4","gravatar_id":"","url":"https://api.github.com/users/michaelgruenstaeudl","html_url":"https://github.com/michaelgruenstaeudl","followers_url":"https://api.github.com/users/michaelgruenstaeudl/followers","following_url":"https://api.github.com/users/michaelgruenstaeudl/following{/other_user}","gists_url":"https://api.github.com/users/michaelgruenstaeudl/gists{/gist_id}","starred_url":"https://api.github.com/users/michaelgruenstaeudl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/michaelgruenstaeudl/subscriptions","organizations_url":"https://api.github.com/users/michaelgruenstaeudl/orgs","repos_url":"https://api.github.com/users/michaelgruenstaeudl/repos","events_url":"https://api.github.com/users/michaelgruenstaeudl/events{/privacy}","received_events_url":"https://api.github.com/users/michaelgruenstaeudl/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-03-22T12:35:32Z","updated_at":"2018-03-22T15:42:54Z","closed_at":null,"author_association":"NONE","body":"I receive the following error when compiling SOAPdenovo2:\r\n\r\n```\r\n~/git/SOAPdenovo2 $ make\r\n\r\npregraph_sparse_63mer.v1.0.3 cleaning done.                         \r\npregraph_sparse_63mer.v1.0.3 objects generated.                    \r\nSOAPdenovo-63mer cleaning done.                              \r\nSOAPdenovo-63mer objects generated.                                \r\nsparsePregraph/io_func.o: In function `read1seqbam(char*, char*, int, samfile_t*, int*) [clone .constprop.58]':\r\nio_func.cpp:(.text+0x47): undefined reference to `samread'\r\nio_func.cpp:(.text+0xe2): undefined reference to `bam_format1_core'\r\nsparsePregraph/io_func.o: In function `read1seqbam(char*, char*, int, samfile_t*, int*)':\r\nio_func.cpp:(.text+0x62a): undefined reference to `samread'\r\nio_func.cpp:(.text+0x6ca): undefined reference to `bam_format1_core'\r\nstandardPregraph/readseq1by1.o: In function `read1seqbam':\r\nreadseq1by1.c:(.text+0xaa7): undefined reference to `samread'\r\nreadseq1by1.c:(.text+0xacc): undefined reference to `bam_format1_core'\r\n/lib64/libbam.a(sam.o): In function `samthreads':\r\n(.text+0x11): undefined reference to `hts_get_format'\r\n(.text+0x2c): undefined reference to `bgzf_mt'\r\n/lib64/libbam.a(sam.o): In function `samopen':\r\n(.text+0x62): undefined reference to `hts_open'\r\n(.text+0xb8): undefined reference to `hts_set_fai_filename'\r\n(.text+0xc9): undefined reference to `sam_hdr_read'\r\n(.text+0xe6): undefined reference to `hts_verbose'\r\n(.text+0x12d): undefined reference to `hts_get_format'\r\n(.text+0x15f): undefined reference to `sam_hdr_write'\r\n(.text+0x169): undefined reference to `hts_verbose'\r\n(.text+0x195): undefined reference to `hts_close'\r\n(.text+0x1c5): undefined reference to `hts_close'\r\n/lib64/libbam.a(sam.o): In function `samclose':\r\n(.text+0x1ea): undefined reference to `bam_hdr_destroy'\r\n(.text+0x1f3): undefined reference to `hts_close'\r\n/lib64/libbam.a(sam.o): In function `samfetch':\r\n(.text+0x23a): undefined reference to `bam_init1'\r\n(.text+0x255): undefined reference to `sam_itr_queryi'\r\n(.text+0x279): undefined reference to `hts_itr_next'\r\n(.text+0x28a): undefined reference to `hts_itr_destroy'\r\n(.text+0x293): undefined reference to `bam_destroy1'\r\n/lib64/libbam.a(sam.o): In function `sampileup':\r\n(.text+0x2d6): undefined reference to `bam_init1'\r\n(.text+0x333): undefined reference to `sam_read1'\r\n(.text+0x354): undefined reference to `bam_destroy1'\r\n/lib64/libbam.a(sam.o): In function `samfaipath':\r\n(.text+0x3ed): undefined reference to `hts_verbose'\r\n(.text+0x3f9): undefined reference to `fai_build'\r\n/lib64/libbam.a(bam_plbuf.o): In function `bam_plbuf_reset':\r\n(.text+0x5): undefined reference to `bam_plp_reset'\r\n/lib64/libbam.a(bam_plbuf.o): In function `bam_plbuf_init':\r\n(.text+0x33): undefined reference to `bam_plp_init'\r\n/lib64/libbam.a(bam_plbuf.o): In function `bam_plbuf_destroy':\r\n(.text+0x59): undefined reference to `bam_plp_destroy'\r\n/lib64/libbam.a(bam_plbuf.o): In function `bam_plbuf_push':\r\n(.text+0x95): undefined reference to `bam_plp_push'\r\n(.text+0xd4): undefined reference to `bam_plp_next'\r\ncollect2: error: ld returned 1 exit status\r\nmake: *** [Makefile:58: SOAPdenovo-63mer] Error 1\r\n```\r\n\r\n**Edit 1**:\r\nHere is my compiler info:\r\n```\r\n~/git/SOAPdenovo2 $ make -v\r\n\r\nGNU Make 4.2.1\r\nBuilt for x86_64-unknown-linux-gnu\r\n```"},"comment":{"url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/comments/375353456","html_url":"https://github.com/aquaskyline/SOAPdenovo2/issues/39#issuecomment-375353456","issue_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/39","id":375353456,"user":{"login":"michaelgruenstaeudl","id":7493028,"avatar_url":"https://avatars0.githubusercontent.com/u/7493028?v=4","gravatar_id":"","url":"https://api.github.com/users/michaelgruenstaeudl","html_url":"https://github.com/michaelgruenstaeudl","followers_url":"https://api.github.com/users/michaelgruenstaeudl/followers","following_url":"https://api.github.com/users/michaelgruenstaeudl/following{/other_user}","gists_url":"https://api.github.com/users/michaelgruenstaeudl/gists{/gist_id}","starred_url":"https://api.github.com/users/michaelgruenstaeudl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/michaelgruenstaeudl/subscriptions","organizations_url":"https://api.github.com/users/michaelgruenstaeudl/orgs","repos_url":"https://api.github.com/users/michaelgruenstaeudl/repos","events_url":"https://api.github.com/users/michaelgruenstaeudl/events{/privacy}","received_events_url":"https://api.github.com/users/michaelgruenstaeudl/received_events","type":"User","site_admin":false},"created_at":"2018-03-22T15:42:54Z","updated_at":"2018-03-22T15:42:54Z","author_association":"NONE","body":"Thanks for your assistance. I downloaded the updated code again and attempted to re-compile. However, a different error occurs during compilation now:\r\n```\r\n$ make\r\npregraph_sparse_63mer.v1.0.3 cleaning done.                         \r\npregraph_sparse_63mer.v1.0.3 objects generated.                    \r\nSOAPdenovo-63mer cleaning done.                              \r\nSOAPdenovo-63mer objects generated.                                \r\n/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 shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam_import.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(sam.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam_pileup.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(faidx.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(knetfile.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(sam_header.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bgzf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(kstring.o): relocation R_X86_64_32 against `.text' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam_aux.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: ./sparsePregraph/inc/libbam.a(razf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC\r\n/usr/bin/ld: final link failed: Nonrepresentable section on output\r\ncollect2: error: ld returned 1 exit status\r\nmake: *** [Makefile:58: SOAPdenovo-63mer] Error 1\r\n```"}}
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