According to hier(7) and almost all other ports, /usr/local/etc is the default location for configuration files. This port installs /usr/local/my.cnf via the /usr/local/etc/rc.d/mysql-server script. For example, on this system with 1072 pkg's installed, only this one finds it necessary to install to /usr/local/: # ll /usr/local/ total 984 drwxr-xr-x 22 root wheel 23 Dec 7 09:46 ./ drwxr-xr-x 17 root wheel 17 Aug 2 22:39 ../ drwxr-xr-x 4 root wheel 2833 Nov 27 22:02 bin/ drwxr-xr-x 2 root wheel 26 Nov 27 10:11 bin32/ drwxr-xr-x 2 root wheel 4 Sep 11 00:52 env/ drwxr-xr-x 47 root wheel 88 Nov 27 10:08 etc/ drwxr-xr-x 388 root wheel 1263 Nov 27 22:02 include/ drwxr-xr-x 3 root wheel 86 Nov 27 10:11 info/ drwxr-xr-x 105 root wheel 3766 Nov 27 22:02 lib/ drwxr-xr-x 5 root wheel 51 Nov 27 10:11 lib32/ drwxr-xr-x 5 root wheel 5 Sep 11 00:52 libdata/ drwxr-xr-x 11 root wheel 68 Nov 22 09:10 libexec/ drwxr-xr-x 5 root wheel 5 Jan 21 2015 llvm33/ drwxr-xr-x 6 root wheel 6 Feb 14 2015 llvm35/ drwxr-xr-x 6 root wheel 6 Sep 28 07:51 llvm36/ drwxr-xr-x 33 root wheel 34 Dec 5 04:15 man/ -rw-r--r-- 1 root wheel 943 Dec 7 09:46 my.cnf drwxr-xr-x 9 root wheel 14 Nov 10 10:48 openjdk8/ drwxr-xr-x 5 root wheel 8 Nov 22 09:10 openssl/ drwxr-xr-x 2 root wheel 71 Dec 4 20:41 sbin/ drwxr-xr-x 166 root wheel 166 Nov 27 22:02 share/ drwxr-xr-x 3 root wheel 3 Oct 2 2014 var/ drwxr-xr-x 4 root wheel 4 Aug 2 09:26 x86_64-portbld-freebsd10.1/ # pkg info |wc -l 1072
Thanks for the report. This actually appears to be happening only on the first run, when there's no database yet. I suspect the culprit is the mysql_install_db.sh invoked on first run and --basedir=/usr/local arg.
Created attachment 170490 [details] fix by adding --keep-my.cnf to mysql_install_db options Patch adds --keep-my.cnf to mysql_install_db options which avoids the unneeded/unwanted/useless creation of /usr/local/my.cnf
Depends on patch for bug #192657
A commit references this bug: Author: feld Date: Thu Jan 19 22:29:06 UTC 2017 New revision: 431919 URL: https://svnweb.freebsd.org/changeset/ports/431919 Log: databases/mysql56: Update to 5.6.35 - Port improvements from MySQL 5.7 port - Use system libs instead of bundled - Fix many open PRs - Change MAINTAINER PR: 216244 192657 198812 199751 205093 PR: 209618 211248 205983 209338 Changes: head/databases/mysql56-client/Makefile head/databases/mysql56-client/files/patch-CMakeLists.txt head/databases/mysql56-client/files/patch-extra_CMakeLists.txt head/databases/mysql56-client/files/patch-man_CMakeLists.txt head/databases/mysql56-client/files/patch-mysys_ssl_my_default.cc head/databases/mysql56-client/files/patch-scripts_CMakeLists.txt head/databases/mysql56-client/files/patch-support-files_CMakeLists.txt head/databases/mysql56-client/pkg-message head/databases/mysql56-server/Makefile head/databases/mysql56-server/distinfo head/databases/mysql56-server/files/my.cnf.sample.in head/databases/mysql56-server/files/mysql-server.in head/databases/mysql56-server/files/patch-mysys_ssl_my_default.cc head/databases/mysql56-server/pkg-message head/databases/mysql56-server/pkg-plist
A commit references this bug: Author: brnrd Date: Thu Jan 26 19:58:06 UTC 2017 New revision: 432535 URL: https://svnweb.freebsd.org/changeset/ports/432535 Log: MFH: r431919 r431968 r431975 r432035 r432066 r432458 databases/mysql56: Update to 5.6.35 - Port improvements from MySQL 5.7 port - Use system libs instead of bundled - Fix many open PRs - Change MAINTAINER PR: 216244 192657 198812 199751 205093 PR: 209618 211248 205983 209338 databases/mysql56-server: Rollback rc script changes databases/mysql56-server: Do not install my.cnf sample An issue was discovered where users of mysql did not have a my.cnf and the recent update was causing mysqld to find a sample my.cnf and load its parameters. This was causing errors on startup for users of innodb as the parameters used to init the database did not match the ones in the sample config file it was now reading. databases/mysql56-server: Fix build with LibreSSL - Fix CMake SSL detection - Always set WITH_SSL=${OPENSSLBASE} PR: 216311 Approved by: Mahdi Moktari <mokhi64@gmail.com> (maintainer) Differential Revision: D9272 Revert r432035 part 2, it breaks build with openssl from base With hat: portmgr databases/mysql56-server: Fix OpenSSL linking - Force dynamic linking with OpenSSL Approved by: ports-secteam (feld) Changes: _U branches/2017Q1/ branches/2017Q1/databases/mysql56-client/Makefile branches/2017Q1/databases/mysql56-client/files/patch-CMakeLists.txt branches/2017Q1/databases/mysql56-client/files/patch-cmake_ssl.cmake branches/2017Q1/databases/mysql56-client/files/patch-extra_CMakeLists.txt branches/2017Q1/databases/mysql56-client/files/patch-man_CMakeLists.txt branches/2017Q1/databases/mysql56-client/files/patch-mysys_ssl_my_default.cc branches/2017Q1/databases/mysql56-client/files/patch-scripts_CMakeLists.txt branches/2017Q1/databases/mysql56-client/files/patch-support-files_CMakeLists.txt branches/2017Q1/databases/mysql56-client/pkg-message branches/2017Q1/databases/mysql56-server/Makefile branches/2017Q1/databases/mysql56-server/distinfo branches/2017Q1/databases/mysql56-server/files/my.cnf.sample.in branches/2017Q1/databases/mysql56-server/files/patch-cmake_ssl.cmake branches/2017Q1/databases/mysql56-server/files/patch-mysys_ssl_my_default.cc branches/2017Q1/databases/mysql56-server/pkg-message branches/2017Q1/databases/mysql56-server/pkg-plist