Hi Jacob, Also, have you set the USE_variables mentioned here: http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables ?
Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group ----- Original Message ----- From: "Mary Goldman" <[email protected]> To: "Jacob C Schwartz" <[email protected]> Cc: [email protected] Sent: Tuesday, October 26, 2010 2:47:08 PM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] install Mac OS X 10.6.4 Hi Jacob, Please try setting you MySQL variables as below: MYSQLINC="/usr/local/mysql/include" MYSQLLIBS="/usr/local/mysql/lib/libmysqlclient.a -lssl -lcrypto -lz" Feel free to contact the mail list again if does not resolve your issue. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group ----- Original Message ----- From: "Jacob C Schwartz" <[email protected]> To: [email protected] Sent: Monday, October 25, 2010 8:22:52 PM GMT -08:00 US/Canada Pacific Subject: [Genome] install Mac OS X 10.6.4 Hi, I've been working to install genome browser and decided to reach out to you guys for help. I've tried several install protocols (that I found on the mail lists but for older version of Mac OS X) and I always get after the final make in the directory jksrc the error as follows (same error for make in jksrc/gfserver or in utils/bedToBigBed): Undefined symbols: "_ERR_load_crypto_strings", referenced from: _netConnectHttps in jkweb.a(https.o) "_BIO_ctrl", referenced from: _netConnectHttps in jkweb.a(https.o) _netConnectHttps in jkweb.a(https.o) _netConnectHttps in jkweb.a(https.o) _netConnectHttps in jkweb.a(https.o) _netConnectHttps in jkweb.a(https.o) "_BIO_read", referenced from: _netConnectHttps in jkweb.a(https.o) "_BIO_free_all", referenced from: _netConnectHttps in jkweb.a(https.o) "_BIO_write", referenced from: _netConnectHttps in jkweb.a(https.o) "_OPENSSL_add_all_algorithms_noconf", referenced from: _netConnectHttps in jkweb.a(https.o) "_ERR_print_errors_fp", referenced from: _netConnectHttps in jkweb.a(https.o) _netConnectHttps in jkweb.a(https.o) _netConnectHttps in jkweb.a(https.o) _netConnectHttps in jkweb.a(https.o) ld: symbol(s) not found collect2: ld returned 1 exit status make[1]: *** [blat] Error 1 So the best protocol I've had is as follows: I installed MySQL (5.1.51) and fink (0.29.10) and openssl (1.0.0a). I'm running Mac OS X 10.6.4 on a Macbook with 2.4 GHz Intel Core 2 Duo. PATH=$PATH:$HOME/bin/x86_64 MACHTYPE=x86_64 MYSQLLIBS="/usr/local/mysql/include/libmysqlclient.a -lz" MYSQLINC=/usr/local/mysql/lib make in lib make in jkownlib sudo mkdir /usr/local/apache/ sudo mkdir /usr/local/apache/cgi-bin-jacobschwartz sudo chown -R jacobschwartz /usr/local/apache/cgi-bin-jacobschwartz sudo mkdir /usr/local/apache/htdocs/ sudo chown -R jacobschwartz /usr/local/apache/htdocs make in jksrc If you have any ideas I would really appreciate it. I can work to install on a different computer (our Linux cluster) but if possible I hoped to install on a simple machine for simple tasks like making bedtobigbed conversions. Thanks so much, Jacob Schwartz Postdoctoral researcher Lab of Tom Cech Department of Chemistry and Biochemistry UC Boulder, CO 80309 _______________________________________________ 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
