Hello Hiram, At first my particular distribution was missing the libmysqlclient.a file. I managed to get that from another one of our servers and set the environment variable to its location.
I used CVS to get the source tree. When I type make in the kent/src/hg/makeDb/hgTrackDb directory I get the following error: gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hgTrackDb.o -c hgTrackDb.c gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /root/bin/x86_64/hgTrackDb hgTrackDb.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lm /usr/lib64/mysql/libmysqlclient.a -lz /usr/lib64/mysql/libmysqlclient.a(client.o): In function `mysql_close_free_options': (.text+0xdb5): undefined reference to `SSL_CTX_free' /usr/lib64/mysql/libmysqlclient.a(client.o): In function `mysql_get_ssl_cipher': (.text+0x1155): undefined reference to `SSL_get_current_cipher' /usr/lib64/mysql/libmysqlclient.a(client.o): In function `mysql_real_connect': (.text+0x3879): undefined reference to `SSL_get_peer_certificate' /usr/lib64/mysql/libmysqlclient.a(client.o): In function `mysql_real_connect': (.text+0x3891): undefined reference to `X509_get_subject_name' /usr/lib64/mysql/libmysqlclient.a(client.o): In function `mysql_real_connect': (.text+0x38a1): undefined reference to `X509_NAME_oneline' /usr/lib64/mysql/libmysqlclient.a(client.o): In function `mysql_real_connect': (.text+0x38a9): undefined reference to `X509_free' /usr/lib64/mysql/libmysqlclient.a(client.o): In function `mysql_get_ssl_cipher': (.text+0x1161): undefined reference to `SSL_CIPHER_get_name' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': (.text+0x54): undefined reference to `SSL_new' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': (.text+0x68): undefined reference to `SSL_clear' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': (.text+0x70): undefined reference to `SSL_get_session' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': (.text+0x7b): undefined reference to `SSL_SESSION_set_timeout' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': (.text+0x86): undefined reference to `SSL_set_fd' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': (.text+0x99): undefined reference to `SSL_get_fd' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': (.text+0x105): undefined reference to `ERR_get_error_line_data' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': (.text+0x112): undefined reference to `SSL_free' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': (.text+0x155): undefined reference to `ERR_get_error_line_data' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `sslconnect': (.text+0x161): undefined reference to `SSL_connect' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `sslaccept': (.text+0x171): undefined reference to `SSL_accept' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_close': (.text+0x1a6): undefined reference to `SSL_set_quiet_shutdown' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_close': (.text+0x1ae): undefined reference to `SSL_shutdown' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_delete': (.text+0x1ec): undefined reference to `SSL_free' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_write': (.text+0x228): undefined reference to `SSL_write' /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_read': (.text+0x238): undefined reference to `SSL_read' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x71): undefined reference to `SSL_CTX_new' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x8e): undefined reference to `SSL_CTX_set_cipher_list' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0xa7): undefined reference to `SSL_CTX_load_verify_locations' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0xc8): undefined reference to `SSL_CTX_use_certificate_file' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0xe7): undefined reference to `SSL_CTX_use_PrivateKey_file' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0xf7): undefined reference to `SSL_CTX_check_private_key' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x107): undefined reference to `DH_new' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x127): undefined reference to `BN_bin2bn' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x13c): undefined reference to `BN_bin2bn' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x167): undefined reference to `SSL_CTX_ctrl' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x16f): undefined reference to `DH_free' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x1a5): undefined reference to `SSL_CTX_set_default_verify_paths' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x1d5): undefined reference to `ERR_get_error_line_data' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x1e5): undefined reference to `SSL_CTX_free' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x208): undefined reference to `SSL_load_error_strings' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x220): undefined reference to `SSL_library_init' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x225): undefined reference to `OPENSSL_add_all_algorithms_noconf' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x278): undefined reference to `ERR_get_error_line_data' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x2d6): undefined reference to `DH_free' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x30d): undefined reference to `ERR_get_error_line_data' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x31b): undefined reference to `SSL_CTX_free' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLFd': (.text+0x35d): undefined reference to `ERR_get_error_line_data' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLAcceptorFd': (.text+0x39d): undefined reference to `TLSv1_server_method' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLAcceptorFd': (.text+0x3d0): undefined reference to `SSL_CTX_ctrl' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLAcceptorFd': (.text+0x3e2): undefined reference to `SSL_CTX_set_verify' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLAcceptorFd': (.text+0x3f2): undefined reference to `SSL_CTX_set_session_id_context' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `vio_verify_callback': (.text+0x452): undefined reference to `X509_STORE_CTX_get_current_cert' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `vio_verify_callback': (.text+0x45a): undefined reference to `X509_get_subject_name' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `vio_verify_callback': (.text+0x46a): undefined reference to `X509_NAME_oneline' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `vio_verify_callback': (.text+0x4b8): undefined reference to `X509_get_issuer_name' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `vio_verify_callback': (.text+0x4c8): undefined reference to `X509_NAME_oneline' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `vio_verify_callback': (.text+0x4d4): undefined reference to `X509_STORE_CTX_get_error' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `vio_verify_callback': (.text+0x4dc): undefined reference to `X509_STORE_CTX_get_error_depth' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLConnectorFd': (.text+0x52d): undefined reference to `TLSv1_client_method' /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function `new_VioSSLConnectorFd': (.text+0x56f): undefined reference to `SSL_CTX_set_verify' collect2: ld returned 1 exit status make: *** [hgTrackDb] Error 1 Abhishek Goel Staff Research Associate Geschwind Laboratory, UCLA Neurology Gonda Neuroscience and Genetics Research Center #2309 University of California Los Angeles 695 Charles E. Young Dr. South Los Angeles, CA 90095 Tel: (310) 794-7537 Fax: (310) 267-2401 On Tue, Nov 10, 2009 at 9:11 PM, Hiram Clawson <[email protected]> wrote: > Please give me a hint on your compile problems. > It should be pretty easy to build the binaries there. > If you are going to be running your own copy of > the genome browser you will want to be able to > build the source tree. Give me an example of > a failed gcc command. > > --Hiram > > Abhishek Goel wrote: > >> Hello Hiram, >> >> Thank you for that information. I've been trying to compile the hgTrackDb >> and hgFindSpec binaries but I keep running into an error. I am trying to >> find some solution for the issue but I was wondering if there were any >> precompiled versions that you had that we could download. Is that a >> possibility? >> >> Thanks >> >> Abhishek >> >> >> Abhishek Goel >> Staff Research Associate >> Geschwind Laboratory, UCLA Neurology >> Gonda Neuroscience and Genetics Research Center #2309 >> University of California Los Angeles >> 695 Charles E. Young Dr. South >> Los Angeles, CA 90095 >> Tel: (310) 794-7537 >> Fax: (310) 267-2401 >> >> >> >> >> >> On Tue, Oct 27, 2009 at 8:35 AM, Hiram Clawson <[email protected]> >> wrote: >> >> Good Morning Abhishek: >>> >>> You should take these tracks and make them permanent tracks >>> in your browser if you would like them to be available to >>> everyone. See these starting notes about how to load tracks >>> into the browser: >>> http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/README.trackDb<http://genome-test.cse.ucsc.edu/%7Ekent/src/unzipped/product/README.trackDb> >>> < >>> http://genome-test.cse.ucsc.edu/%7Ekent/src/unzipped/product/README.trackDb >>> > >>> >>> >>> Follow the additional references to other README files from there. >>> >>> --Hiram >>> >>> >>> Abhishek Goel wrote: >>> >>> Hello Jennifer, >>>> >>>> Thank you for that info. Do you have any suggestions on where to start. >>>> I >>>> was going to see if there was any table with the list of hgsids but it >>>> turns >>>> out those are just temp ids and not really useful. >>>> >>>> Each time a BED file is loaded into the browser to create a custom track >>>> a >>>> new table is added to the customTrash database. The table itself is just >>>> the >>>> mysql version of the BED file. >>>> >>>> Thanks. >>>> >>>> Abhishek >>>> >>>> >>>> Abhishek Goel >>>> Staff Research Associate >>>> Geschwind Laboratory, UCLA Neurology >>>> Gonda Neuroscience and Genetics Research Center #2309 >>>> University of California Los Angeles >>>> 695 Charles E. Young Dr. South >>>> Los Angeles, CA 90095 >>>> Tel: (310) 794-7537 >>>> Fax: (310) 267-2401 >>>> >>>> >>>> >>>> >>>> >>>> On Thu, Oct 22, 2009 at 5:42 PM, Jennifer Jackson <[email protected]> >>>> wrote: >>>> >>>> Hello, >>>> >>>>> No, there is no automatically generated page. The idea of making one >>>>> from >>>>> the custom track table is a good one. >>>>> >>>>> The only alternative would be to get wiki and Sessions set up, but that >>>>> is >>>>> a major project, and not worth it for just a web page view. >>>>> >>>>> Hope this helps, >>>>> Jennifer >>>>> >>>>> >>>>> ------------------------------------------------ >>>>> Jennifer Jackson >>>>> UCSC Genome Bioinformatics Group >>>>> >>>>> ----- "Abhishek Goel" <[email protected]> wrote: >>>>> >>>>> From: "Abhishek Goel" <[email protected]> >>>>> >>>>>> To: [email protected] >>>>>> Sent: Thursday, October 22, 2009 12:29:28 PM GMT -08:00 US/Canada >>>>>> Pacific >>>>>> Subject: [Genome] Saved custom tracks >>>>>> >>>>>> Hello, >>>>>> >>>>>> I've just set up a Genome Browser mirror for our lab and our >>>>>> collaborators. >>>>>> I enabled the customTrash database and set up the hg.conf file so that >>>>>> the >>>>>> added customTracks are saved. However, is there a page that lists all >>>>>> the >>>>>> custom tracks that have been saved? >>>>>> >>>>>> I could just create a page that would list all the saved custom tracks >>>>>> from >>>>>> the mysql database but I thought if there is already a page I could >>>>>> just use >>>>>> that. >>>>>> >>>>>> Thanks. >>>>>> >>>>>> Abhishek >>>>>> >>>>>> Abhishek Goel >>>>>> Staff Research Associate >>>>>> Geschwind Laboratory, UCLA Neurology >>>>>> Gonda Neuroscience and Genetics Research Center #2309 >>>>>> University of California Los Angeles >>>>>> 695 Charles E. Young Dr. South >>>>>> Los Angeles, CA 90095 >>>>>> Tel: (310) 794-7537 >>>>>> Fax: (310) 267-2401 >>>>>> _______________________________________________ >>>>>> Genome maillist - [email protected] >>>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>>>> >>>>>> _______________________________________________ >>>>> >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>> >>>> >>>> >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
