databases/mariadb101-client upgraded in wrong order, resulted in missing files

Fri Mar 31 13:31:39 UTC 2017

I don't know if it was "pkg" fault or mariadb101-server and 
mariadb101-client conflict.

I did standard "pkg upgrade" and at the end I have half files of 
mariadb101-client missing:

# pkg check -Ba
Checking all packages: ...
pkg: fstat() failed for(/usr/local/bin/msql2mysql): No such file or 
directory
pkg: fstat() failed for(/usr/local/bin/mysql_find_rows): No such file or 
directory
pkg: fstat() failed for(/usr/local/bin/mysqlaccess): No such file or 
directory
pkg: fstat() failed for(/usr/local/include/mysql/big_endian.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/byte_order_generic.h): 
No such file or directory
pkg: fstat() failed 
for(/usr/local/include/mysql/byte_order_generic_x86.h): No such file or 
directory
pkg: fstat() failed 
for(/usr/local/include/mysql/byte_order_generic_x86_64.h): No such file 
or directory
pkg: fstat() failed for(/usr/local/include/mysql/client_plugin.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/decimal.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/errmsg.h): No such file 
or directory
pkg: fstat() failed for(/usr/local/include/mysql/handler_ername.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/handler_state.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/keycache.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/little_endian.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/m_ctype.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/ma_dyncol.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_alloc.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_attribute.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_byteorder.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_compiler.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_dbug.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_dir.h): No such file 
or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_getopt.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_list.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_net.h): No such file 
or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_pthread.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/my_xml.h): No such file 
or directory
pkg: fstat() failed for(/usr/local/include/mysql/mysql_com.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/mysql_com_server.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/mysql_embed.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/mysql_time.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/mysqld_ername.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/mysqld_error.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/plugin_audit.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/plugin_auth_common.h): 
No such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/plugin_encryption.h): 
No such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/plugin_ftparser.h): No 
such file or directory
pkg: fstat() failed 
for(/usr/local/include/mysql/plugin_password_validation.h): No such file 
or directory
pkg: fstat() failed for(/usr/local/include/mysql/psi/mysql_idle.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/psi/mysql_socket.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/psi/mysql_stage.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/psi/mysql_statement.h): 
No such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/psi/mysql_table.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/psi/mysql_thread.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/service_debug_sync.h): 
No such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/service_encryption.h): 
No such file or directory
pkg: fstat() failed 
for(/usr/local/include/mysql/service_encryption_scheme.h): No such file 
or directory
pkg: fstat() failed 
for(/usr/local/include/mysql/service_kill_statement.h): No such file or 
directory
pkg: fstat() failed for(/usr/local/include/mysql/service_md5.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/service_my_snprintf.h): 
No such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/service_sha1.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/service_thd_alloc.h): 
No such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/service_thd_autoinc.h): 
No such file or directory
pkg: fstat() failed 
for(/usr/local/include/mysql/service_thd_error_context.h): No such file 
or directory
pkg: fstat() failed 
for(/usr/local/include/mysql/service_thd_specifics.h): No such file or 
directory
pkg: fstat() failed 
for(/usr/local/include/mysql/service_thd_timezone.h): No such file or 
directory
pkg: fstat() failed for(/usr/local/include/mysql/service_thd_wait.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/service_wsrep.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/sql_common.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/sql_state.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/sslopt-case.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/sslopt-longopts.h): No 
such file or directory
pkg: fstat() failed for(/usr/local/include/mysql/sslopt-vars.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/include/mysql/typelib.h): No such 
file or directory
pkg: fstat() failed for(/usr/local/lib/mysql/libmysqlclient.so): No such 
file or directory
pkg: fstat() failed for(/usr/local/lib/mysql/libmysqlclient_r.a): No 
such file or directory
pkg: fstat() failed for(/usr/local/lib/mysql/libmysqlclient_r.so): No 
such file or directory
pkg: fstat() failed for(/usr/local/lib/mysql/libmysqlclient_r.so.18): No 
such file or directory
pkg: fstat() failed for(/usr/local/lib/mysql/plugin/daemon_example.ini): 
No such file or directory
pkg: fstat() failed for(/usr/local/lib/mysql/plugin/dialog.so): No such 
file or directory
pkg: fstat() failed 
for(/usr/local/lib/mysql/plugin/mysql_clear_password.so): No such file 
or directory
pkg: fstat() failed for(/usr/local/libdata/ldconfig/mariadb101-client): 
No such file or directory
pkg: fstat() failed for(/usr/local/man/man1/msql2mysql.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysql.1.gz): No such file or 
directory
pkg: fstat() failed for(/usr/local/man/man1/mysql_config.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysql_find_rows.1.gz): No 
such file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysql_plugin.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysql_waitpid.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysqlaccess.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysqlbinlog.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysqlcheck.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysqldump.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysqlimport.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysqlshow.1.gz): No such 
file or directory
pkg: fstat() failed for(/usr/local/man/man1/mysqlslap.1.gz): No such 
file or directory
Checking all packages.......... done

I think this is the root cause

Checking integrity... done (2 conflicting)
   - mariadb101-server-10.1.22 conflicts with mariadb101-client-10.1.21 
on /usr/local/share/mysql/maria_add_gis_sp.sql

[51/86] Installing mariadb101-client-10.1.22...
[51/86] Extracting mariadb101-client-10.1.22: .......... done
..
..
[69/86] Deinstalling mariadb101-client-10.1.21...
[69/86] Deleting files for mariadb101-client-10.1.21:
pkg: /usr/local/bin/mysql different from original checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/bin/mysql_config different from original checksum, not 
removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/bin/mysqladmin different from original checksum, not 
removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/bin/mysqlbinlog different from original checksum, not 
removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/bin/mysqlcheck different from original checksum, not 
removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/bin/mysqldump different from original checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/bin/mysqlimport different from original checksum, not 
removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/bin/mysqlshow different from original checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/bin/mysqlslap different from original checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/auth_dialog_client.h different from 
original checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21.....
pkg: /usr/local/include/mysql/m_string.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/my_config.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/my_decimal_limits.h different from 
original checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21....
pkg: /usr/local/include/mysql/my_global.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/my_sys.h different from original checksum, 
not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/my_valgrind.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/mysql.h different from original checksum, 
not removing
[69/86] Deleting files for mariadb101-client-10.1.21....
pkg: /usr/local/include/mysql/mysql_version.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/plugin.h different from original checksum, 
not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/plugin_auth.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21....
pkg: /usr/local/include/mysql/psi/mysql_file.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/psi/psi.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21....
pkg: /usr/local/include/mysql/service_logger.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/include/mysql/service_progress_report.h different from 
original checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21....
pkg: /usr/local/include/mysql/services.h different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/lib/mysql/libmysqlclient.a different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21...
pkg: /usr/local/lib/mysql/libmysqlclient.so.18 different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21.....
pkg: /usr/local/man/man1/mysqladmin.1.gz different from original 
checksum, not removing
[69/86] Deleting files for mariadb101-client-10.1.21.... done
..
..
[82/86] Upgrading mariadb101-server from 10.1.21 to 10.1.22...
===> Creating groups.
Using existing group 'mysql'.
===> Creating users
Using existing user 'mysql'.
[82/86] Extracting mariadb101-server-10.1.22: .......... done

This was on FreeBSD 10.3 amd64 with packages from own poudriere with 
follogin settings:

OPTIONS_UNSET= X11 GUI CUPS DOCS EXAMPLES NLS HAL
WITH_BDB_VER=5
WITH_GHOSTSCRIPT_VER=9
DEFAULT_VERSIONS=apache=2.4 perl5=5.24 mysql=10.1m php=5.6 python=2.7 
python3=3.5 pgsql=9.4 ssl=openssl
DISABLE_LICENSES=yes

databases_mariadb101-client/options
OPTIONS_FILE_SET+=GSSAPI_NONE

databases_mariadb101-server/options
OPTIONS_FILE_SET+=MAXKEY
OPTIONS_FILE_SET+=GSSAPI_NONE
OPTIONS_FILE_SET+=SPHINX
OPTIONS_FILE_SET+=SPIDER

I think all users of MariaDB 10.1 should be warned in UPDATING

Let me know if you need some more details.

Miroslav Lachman