Closed taoqxtaozi closed 11 months ago
the cc command is missing -lssl and something to include htslib. I don't know this makefile, it's not ours. Your system may also be missing the openssl and htslib libraries? You can paste the "cc" command into a terminal and play with it until it works. Let us know if you find out what the problem was.
We have the kent-core repository and the "user-apps" tarball distribution to help with building for third party projects, but here it's not a problem with our own build process but rather something in the third-party app. You can also contact the author of mafJoin and ask them.
On Mon, Nov 6, 2023 at 10:19 AM 'taoqxtaozi' via UCSC Genome Browser Confidential Support @.***> wrote:
Hi,
I try to use MafJion https://github.com/dentearl/mafJoin, and it need kent, and I meet this problem:
cc -O3 -g -Wall -Werror --pedantic -funroll-loops -lm -DNDEBUG -Wno-error -I ../sonLib/lib -I ./src -I ../kent-master/src/inc -std=c99 -pedantic -o bin/mafJoin.tmp obj/mafJoin.o obj/jkmaf.o obj/genome.o obj/mafTree.o obj/malnComp.o obj/malnBlk.o obj/malnBlkCursor.o obj/malnBlkSet.o obj/malnSet.o obj/malnJoinBlks.o obj/malnJoinWithinSet.o obj/malnJoinSets.o obj/malnMergeComps.o obj/malnMultiParents.o obj/malnCompCompMap.o obj/malnAdjust.o ../kent-master/src/lib/x86_64/jkweb.a ../sonLib/lib/sonLib.a ../kent-master/src/lib/x86_64/jkweb.a(linefile.o): In function
lineFileTabixAndIndexMayOpen': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:241: undefined reference to
hts_open' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:248: undefined reference totbx_index_load2' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:268: undefined reference to
tbx_readrec' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:268: undefined reference tohts_itr_query' ../kent-master/src/lib/x86_64/jkweb.a(linefile.o): In function
lineFileSetTabixRegion': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:280: undefined reference totbx_name2id' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:293: undefined reference to
tbx_readrec' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:293: undefined reference tohts_itr_query' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:297: undefined reference to
hts_itr_destroy' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:283: undefined reference totbx_name2id' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:287: undefined reference to
tbx_name2id' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:289: undefined reference totbx_name2id' ../kent-master/src/lib/x86_64/jkweb.a(linefile.o): In function
lineFileNext': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:567: undefined reference tohts_get_bgzfp' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:567: undefined reference to
hts_itr_next' ../kent-master/src/lib/x86_64/jkweb.a(linefile.o): In functionlineFileClose': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:722: undefined reference to
hts_itr_destroy' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:723: undefined reference totbx_destroy' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/linefile.c:724: undefined reference to
hts_close' ../kent-master/src/lib/x86_64/jkweb.a(udc.o): In functionaddElementToDy': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/udc.c:1212: undefined reference to
SHA1' ../kent-master/src/lib/x86_64/jkweb.a(net.o): In functionsendFtpDataToPipeThread': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/net.c:1093: undefined reference to
pthread_detach' ../kent-master/src/lib/x86_64/jkweb.a(net.o): In functionnetGetOpenFtpSockets': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/net.c:1263: undefined reference to
pthread_create' ../kent-master/src/lib/x86_64/jkweb.a(https.o): In functionnetConnectHttpsThread': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:135: undefined reference to
pthread_detach' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:159: undefined reference toBIO_ctrl' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:213: undefined reference to
BIO_write' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:216: undefined reference toBIO_test_flags' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:218: undefined reference to
ERR_print_errors_fp' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:237: undefined reference toBIO_read' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:241: undefined reference to
BIO_test_flags' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:276: undefined reference toBIO_free_all' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:249: undefined reference to
ERR_print_errors_fp' ../kent-master/src/lib/x86_64/jkweb.a(https.o): In functionverify_callback': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:293: undefined reference to
X509_STORE_CTX_get_current_cert' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:294: undefined reference toX509_STORE_CTX_get_error' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:295: undefined reference to
X509_STORE_CTX_get_error_depth' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:302: undefined reference toX509_get_subject_name' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:302: undefined reference to
X509_NAME_oneline' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:314: undefined reference toSSL_get_ex_data_X509_STORE_CTX_idx' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:314: undefined reference to
X509_STORE_CTX_get_ex_data' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:315: undefined reference toSSL_get_ex_data' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:322: undefined reference to
X509_STORE_CTX_set_error' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:332: undefined reference toX509_verify_cert_error_string' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:340: undefined reference to
X509_verify_cert_error_string' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:348: undefined reference toX509_get_issuer_name' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:348: undefined reference to
X509_NAME_oneline' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:342: undefined reference toX509_verify_cert_error_string' ../kent-master/src/lib/x86_64/jkweb.a(https.o): In function
openSslInit': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:115: undefined reference toOPENSSL_init_ssl' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:116: undefined reference to
OPENSSL_init_crypto' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:117: undefined reference toERR_load_SSL_strings' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:118: undefined reference to
OPENSSL_init_crypto' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:120: undefined reference toCRYPTO_get_ex_new_index' ../kent-master/src/lib/x86_64/jkweb.a(https.o): In function
netConnectHttps': /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:604: undefined reference toTLS_client_method' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:604: undefined reference to
SSL_CTX_new' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:630: undefined reference toSSL_CTX_get0_param' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:631: undefined reference to
X509_VERIFY_PARAM_set_hostflags' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:632: undefined reference toX509_VERIFY_PARAM_set1_host' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:641: undefined reference to
SSL_CTX_get_cert_store' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:641: undefined reference toX509_STORE_set_flags' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:650: undefined reference to
SSL_CTX_set_verify' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:656: undefined reference toSSL_CTX_set_verify_depth' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:659: undefined reference to
SSL_CTX_set_default_verify_paths' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:840: undefined reference toBIO_free_all' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:748: undefined reference to
SSL_set_ex_data' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:759: undefined reference toSSL_ctrl' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:772: undefined reference to
ERR_get_error' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:772: undefined reference toERR_reason_error_string' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:788: undefined reference to
BIO_test_flags' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:765: undefined reference toBIO_ctrl' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:769: undefined reference to
BIO_test_flags' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:776: undefined reference toBIO_ctrl' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:784: undefined reference to
BIO_test_flags' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:827: undefined reference topthread_create' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:604: undefined reference to
TLS_client_method' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:604: undefined reference toSSL_CTX_new' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:726: undefined reference to
BIO_new_socket' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:733: undefined reference toBIO_new_ssl' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:739: undefined reference to
BIO_push' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:740: undefined reference toBIO_ctrl' /mnt/c/f/Download/software/try_evolver/kent-master/src/lib/https.c:761: undefined reference to
BIO_ctrl' collect2: error: ld returned 1 exit status Makefile:43: recipe for target 'bin/mafJoin' failed make: *** [bin/mafJoin] Error 1I check the libs and find nothing wrong, so looking forward to some reply.
Thanks!
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Hi, thanks for replying! The author of mafJoin replied me, I tried adding -lssl and other libraries, and it finally worked. Thanks!
Hi,
I try to use MafJion https://github.com/dentearl/mafJoin, and it need kent, and I meet this problem:
I check the libs and find nothing wrong, so looking forward to some reply.
Thanks!