よろしくお願いいたします。

3.Alpha.13g
CWD: /Applications/khcoder3
MacOS High Sierra 10.13.6

■エラー
（１）KH Coderの起動に非常に時間がかかり、起動したあと「新規プロジェクト」「プロジェクトを開く」で落ちます。ファイル参照を指定してOKボタンを押すとフリーズして、しばらくして強制終了します。
（２）インストールしてから最初の1回だけ少し動きましたが、チュートリアルkokoroのjpファイルを開いて前処理をして少ししたら落ちました。

■効果がなかったこと
Macの再起動
KH Coderの再インストール
XQuartzの再インストール
MacUIMの再インストール

■備考
（１）[No.1629] [Mac] 新規プロジェクトで落ちます　と似ているように思いますが、回答の「kh_lib/kh_projects.pmをテキストエディタで開き、112行目を見ると以下のような記述があります。」という記述にあるkh_projects.pmというファイルが見当たらず、スレッドにあるアドバイスは試していません。
（２）6月ごろに初めてインストールした直後、数日使用した際には、問題なく作動しました。
その後、フォルダ等の場所を移動したりなどはしていませんが、最近になって必要があり起動したところエラーが起きたため、再インストール等試しましたが、解決しませんでした。

■コンソール・ウィンドウの表示内容
・エラー（２）の場合
khcoder ***error for object 0x7ffeefbfdf60: ponter being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
bash: line 1: 3173 Abort trap: 6

・エラー（１）の場合
This is KH Coder 3.Alpha.13g on darwin.
CWD: /Applications/khcoder3
Executing Mac OS X 64-bit Package
Checking MySQL connection...
Starting MySQL...
uim <-> XIM bridge. Supporting multiple locales.
Using full-synchronous XIM event flow
2018-10-29 12:20:23 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2018-10-29 12:20:23 3083 [Warning] Setting lower_case_table_names=2 because file system for /Applications/khcoder3/deps/mysql-5.6.17/data/ is case insensitive
2018-10-29 12:20:23 3083 [Note] Plugin 'FEDERATED' is disabled.
2018-10-29 12:20:23 3083 [Note] InnoDB: Using atomics to ref count buffer pool pages
2018-10-29 12:20:23 3083 [Note] InnoDB: The InnoDB memory heap is disabled
2018-10-29 12:20:23 3083 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2018-10-29 12:20:23 3083 [Note] InnoDB: Compressed tables use zlib 1.2.3
2018-10-29 12:20:23 3083 [Note] InnoDB: Using CPU crc32 instructions
2018-10-29 12:20:23 3083 [Note] InnoDB: Initializing buffer pool, size = 512.0M
2018-10-29 12:20:23 3083 [Note] InnoDB: Completed initialization of buffer pool
2018-10-29 12:20:23 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:23 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:23 3083 [Note] InnoDB: Retrying to lock the first data file
2018-10-29 12:20:24 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:24 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:25 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:25 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:26 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:26 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:27 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:27 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:28 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:28 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:29 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:29 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:30 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:30 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:31 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:31 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:32 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:32 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:33 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:33 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:34 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:34 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:35 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:35 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:36 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:36 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:37 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:37 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
Supported conversion engines:
direct (*)
yahoo-jp (ja)
baidu-olime-jp (ja)
google-cgiapi-jp (ja)
social-ime (ja)
ajax-ime (ja)
look ()
ipa-x-sampa ()
viqr (vi)
pinyin-big5 (zh_TW:zh_HK)
pyunihan (zh)
py (zh_CN)
wb86 (zh_CN:zh_TW:zh_HK)
zm (zh_CN:zh_TW:zh_HK)
m17n-am-sera (am)
m17n-ar-kbd (ar)
m17n-as-inscript (as)
m17n-as-itrans (as)
m17n-as-phonetic (as)
m17n-ath-phonetic (ath)
m17n-be-kbd (be)
m17n-bla-phonetic (bla)
m17n-bn-inscript (bn)
m17n-bn-itrans (bn)
m17n-bn-probhat (bn)
m17n-bn-unijoy (bn)
m17n-bo-ewts (bo)
m17n-bo-tcrc (bo)
m17n-bo-wylie (bo)
m17n-latn-post (*)
m17n-latn-pre (*)
m17n-rfc1345 (*)
m17n-syrc-phonetic (*)
m17n-unicode (*)
m17n-cmc-kbd (cmc)
m17n-cr-western (cr)
m17n-cs-kbd (cs)
m17n-da-post (da)
m17n-dv-phonetic (dv)
m17n-el-kbd (el)
m17n-eo-h-fundamente (eo)
m17n-eo-h-sistemo (eo)
m17n-eo-plena (eo)
m17n-eo-q-sistemo (eo)
m17n-eo-vi-sistemo (eo)
m17n-eo-x-sistemo (eo)
m17n-fa-isiri (fa)
m17n-fr-azerty (fr)
m17n-grc-mizuochi (grc)
m17n-gu-inscript (gu)
m17n-gu-itrans (gu)
m17n-gu-phonetic (gu)
m17n-he-kbd (he)
m17n-hi-inscript (hi)
m17n-hi-itrans (hi)
m17n-hi-phonetic (hi)
m17n-hi-remington (hi)
m17n-hi-typewriter (hi)
m17n-hi-vedmata (hi)
m17n-hr-kbd (hr)
m17n-hy-kbd (hy)
m17n-ii-phonetic (ii)
m17n-en-ispell (en)
m17n-iu-phonetic (iu)
m17n-ja-anthy (ja)
m17n-ja-tcode (ja)
m17n-ja-trycode (ja)
m17n-ka-kbd (ka)
m17n-kk-arabic (kk)
m17n-kk-kbd (kk)
m17n-km-yannis (km)
m17n-kn-inscript (kn)
m17n-kn-itrans (kn)
m17n-kn-kgp (kn)
m17n-ko-han2 (ko)
m17n-ko-romaja (ko)
m17n-ks-inscript (ks)
m17n-ks-kbd (ks)
m17n-lo-kbd (lo)
m17n-lo-lrt (lo)
m17n-ml-inscript (ml)
m17n-ml-itrans (ml)
m17n-ml-mozhi (ml)
m17n-ml-swanalekha (ml)
m17n-mr-inscript (mr)
m17n-mr-itrans (mr)
m17n-mr-phonetic (mr)
m17n-my-kbd (my)
m17n-ne-rom (ne)
m17n-ne-trad (ne)
m17n-nsk-phonetic (nsk)
m17n-oj-phonetic (oj)
m17n-or-inscript (or)
m17n-or-itrans (or)
m17n-or-phonetic (or)
m17n-pa-inscript (pa)
m17n-pa-itrans (pa)
m17n-pa-jhelum (pa)
m17n-pa-phonetic (pa)
m17n-ps-phonetic (ps)
m17n-ru-kbd (ru)
m17n-ru-phonetic (ru)
m17n-ru-translit (ru)
m17n-ru-yawerty (ru)
m17n-sa-harvard-kyoto (sa)
m17n-sa-IAST (sa)
m17n-sd-inscript (sd)
m17n-si-phonetic-dynamic (si)
m17n-si-samanala (si)
m17n-si-singlish (si)
m17n-si-sumihiri (si)
m17n-si-transliteration (si)
m17n-si-wijesekera (si)
m17n-sk-kbd (sk)
m17n-sr-kbd (sr)
m17n-sv-post (sv)
m17n-ta-inscript (ta)
m17n-ta-itrans (ta)
m17n-ta-lk-renganathan (ta)
m17n-ta-phonetic (ta)
m17n-ta-tamil99 (ta)
m17n-ta-typewriter (ta)
m17n-ta-vutam (ta)
m17n-tai-sonla-kbd (tai)
m17n-te-apple (te)
m17n-te-inscript (te)
m17n-te-itrans (te)
m17n-te-pothana (te)
m17n-te-rts (te)
m17n-th-kesmanee (th)
m17n-th-pattachote (th)
m17n-th-tis820 (th)
m17n-ua-kbd (ua)
m17n-ug-kbd (ug)
m17n-ur-phonetic (ur)
m17n-uz-kbd (uz)
m17n-vi-han (vi)
m17n-vi-nomvni (vi)
m17n-vi-nomtelex (vi)
m17n-vi-tcvn (vi)
m17n-vi-telex (vi)
m17n-vi-viqr (vi)
m17n-vi-vni (vi)
m17n-yi-yivo (yi)
m17n-zh-bopomofo (zh)
m17n-zh-cangjie (zh)
m17n-zh-pinyin-vi (zh)
m17n-zh-pinyin (zh)
m17n-zh-py-b5 (zh)
m17n-zh-py-gb (zh)
m17n-zh-py (zh)
m17n-zh-quick (zh)
m17n-zh-tonepy-b5 (zh)
m17n-zh-tonepy-gb (zh)
m17n-zh-tonepy (zh)
elatin ()
latin ()
byeoru (ko)
tutcode (ja)
skk (ja)
prime (ja)
anthy-utf8 (ja)
anthy (ja)
mozc (ja)
2018-10-29 12:20:38 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:38 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
XMODIFIERS=@im=uim registered, selecting anthy (ja) as default conversion engine
2018-10-29 12:20:39 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:39 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
R Version: 3.1, x86_64
Using un-threaded functions...
2018-10-29 12:20:40 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:40 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:41 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:41 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:42 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:42 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:43 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:43 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:44 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:44 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:45 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:45 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:46 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:46 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:47 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:47 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:48 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:48 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:49 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:49 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:50 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:50 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:51 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:51 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:52 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:52 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:53 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:53 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:54 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:54 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:55 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:55 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:56 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:56 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:57 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:57 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:58 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:58 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:20:59 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:20:59 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:00 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:00 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:01 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:01 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:02 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:02 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:03 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:03 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:04 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:04 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:05 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:05 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:06 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:06 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:07 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:07 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:08 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:08 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:09 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:09 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:10 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:10 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:11 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:11 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:12 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:12 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:13 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:13 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:14 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:14 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:15 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:15 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:16 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:16 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:17 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:17 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:18 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:18 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:19 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:19 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:20 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:20 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:21 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:21 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:22 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:22 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:23 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:23 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:24 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:24 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:25 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:25 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:26 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:26 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:27 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:27 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:28 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:28 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:29 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:29 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:30 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:30 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:31 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:31 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:32 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:32 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:33 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:33 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:34 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:34 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:35 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:35 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:36 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:36 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:37 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:37 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:38 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:38 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:39 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:39 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:40 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:40 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:41 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:41 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:42 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:42 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:43 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:43 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:44 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:44 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:45 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:45 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:46 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:46 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:47 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:47 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:48 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:48 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:49 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:49 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:50 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:50 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:51 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:51 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:52 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:52 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:53 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:53 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:54 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:54 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:55 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:55 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:56 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:56 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:57 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:57 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:58 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:58 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:21:59 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:21:59 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:22:00 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:22:00 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:22:01 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:22:01 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:22:02 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:22:02 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:22:03 3083 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-29 12:22:03 3083 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-29 12:22:03 3083 [Note] InnoDB: Unable to open the first data file
2018-10-29 12:22:03 7fff8af40380 InnoDB: Operating system error number 35 in a file operation.
InnoDB: Error number 35 means 'Resource temporarily unavailable'.
InnoDB: Some operating system error numbers are described at
InnoDB: http://dev.mysql.com/doc/refman/5.6/en/operating-system-error-codes.html
2018-10-29 12:22:03 3083 [ERROR] InnoDB: Can't open './ibdata1'
2018-10-29 12:22:03 3083 [ERROR] InnoDB: Could not open or create the system tablespace. If you tried to add new data files to the system tablespace, and it failed here, you should now edit innodb_data_file_path in my.cnf back to what it was, and remove the new ibdata files InnoDB created in this failed attempt. InnoDB only wrote those files full of zeros, but did not yet use them in any way. But be careful: do not remove old data files which contain your precious data!
2018-10-29 12:22:03 3083 [ERROR] Plugin 'InnoDB' init function returned error.
2018-10-29 12:22:03 3083 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2018-10-29 12:22:03 3083 [ERROR] Unknown/unsupported storage engine: InnoDB
2018-10-29 12:22:03 3083 [ERROR] Aborting

2018-10-29 12:22:03 3083 [Note] Binlog end
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'partition'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_METRICS'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_CMPMEM'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_CMP'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_LOCKS'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'INNODB_TRX'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'BLACKHOLE'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'ARCHIVE'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'MRG_MYISAM'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'MyISAM'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'MEMORY'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'CSV'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'sha256_password'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'mysql_old_password'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'mysql_native_password'
2018-10-29 12:22:03 3083 [Note] Shutting down plugin 'binlog'
2018-10-29 12:22:03 3083 [Note] deps/MySQL-5.6.17/bin/mysqld: Shutdown complete

補足します。

・インストールは「自動設定ソフトウェア（有償サポート）」を使用しました。
・３台のMacにインストールして試しましたが、いずれも同様の症状でした。
・使用したMacのOSはいずれも、MacOS High Sierra 10.13.6です。

インストールの手順は下記ページを見ながら行いました。
http://khcoder.net/mac_com.html

行ったインストールの手順
１，「XQuartz」をインストール、再起動
２，「MacUIM」をインストール、再起動
３，Zipファイルの展開
４，「OK」を確認してターミナル画面を閉じる
５，「khcoder3」フォルダをApplicationフォルダへまるごと移動
６．Set upをクリック
７，「You are ready to run...」を確認
８，kh_coderをクリックして起動

上記の手順は問題なく終了しました。


「Mac版自動設定ソフトウェアのFAQ」ページも確認しましたが、
解決しませんでした。
複数モニタは使用していません。
チュートリアルのファイルでも正常に作動しません。

よろしくお願いいたします。

こんにちは、樋口です。書き込みありがとうございます。

（1）についてですが、InnoDB（=MySQL）のエラーが出ていますね。
「[ERROR] InnoDB」で始まる行です。これらの行が出ているうちはKH Coderは
正常動作しないと思います。

一度Macを再起動してもこのエラーが消えない場合には、KH Coderを完全に削
除してから、再度解凍していただくのが良いかと思います。

1. 「アプリケーション」の中にある「khcoder3」フォルダを削除してください。
2. もし「ダウンロード」フォルダにも「khcoder3」がある場合、これも削除してください。
3. 画面左上隅のリンゴマークからMacを再起動してください。
4. 再度KH Coderの自動設定ソフトウェアをダウンロード・解凍してください。

これでKH Coder起動時のInnoDBのエラーが消えるかどうか見てみてください。

KH Coder再インストール前に、完全削除とMacの再起動を行うのがポイントです。
まずは以上の手順によって「[ERROR] InnoDB」が消えるかどうか、お試しいただいて
結果をお知らせいただけますでしょうか。

あと、なにかセキュリティ・ウイルス対策系のソフトはインストールしていら
っしゃるでしょうか？　これに限らず、動作していた6月頃以降にインストール
なさったアプリなど、思い当たるものはありますか？

p.s.
なお、KH Coderを同時に複数起動することは避けてください。またKH Coderが
起動している際にMacを終了することも避けて下さい。KH Coderを正常終了
させてから（MySQLをShutdownさせてから）、Macを終了するようご注意ください。

こんにちは、樋口です。書き込みありがとうございます。

先ほど書き忘れたのですが、「Applicationフォルダへまるごと移動」をせずに
ダウンロードフォルダに置いたまま「setup」「kh_coder」をダブルクリックし
てみるといかがでしょう。

「Application」のような共有フォルダではなく、ホーム以下（個人フォルダ）
でお試しいただくのも一手かと思いまして。

樋口先生、こんばんは。
ご回答いただきありがとうございます。
ご指示に従い、部分的に解決いたしました。

部分的、と言いますのは、念の為と思い、３台それぞれで確認したところ、
うち１台で、正常に作動いたしません。

このたび３台で試したのは、KH Coderを同時に複数台のPCで起動させる意図はなく、
メインのPCでうまく起動しなかったので、他のPCならどうかと思い、順に試したのですが、
現在は、メインのPCでのみ、問題が解決しません。

問題が解決したPCは、下記のご指示に従って再インストールを行いました。

（ここから引用）
1. 「アプリケーション」の中にある「khcoder3」フォルダを削除してください。
2. もし「ダウンロード」フォルダにも「khcoder3」がある場合、これも削除してください。
3. 画面左上隅のリンゴマークからMacを再起動してください。
4. 再度KH Coderの自動設定ソフトウェアをダウンロード・解凍してください。
（引用ここまで）

これまで失敗していた理由は、以下の２つのようです。
１，KH Coder再インストール前に、完全削除は行ったものの、Macの再起動を同じタイミングで行わなかったため。
２，セキュリティソフト（eset）を起動したままインストールを試みたため。

原因を確かめようと思い、１だけ対処してみましたが、うまくいきませんでした。
２だけ対処しても、うまくいきませんでした。
１と２の両方で解決いたしました。


しかし、それでも１台のみ正常に作動いたしません。
・KH Coderを正常終了させてから、Macを再起動いたしました。
・ダウンロードフォルダに置いたまま「setup」「kh_coder」をダブルクリックしました。
・コンソールで、下記のような記述が得られました。

creating project list... ok
x_mac64(593,0x7fff8f139380) malloc: *** error for object 0x7ffeefbfdf50: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
bash: line 1: 593 Abort trap: 6 ./x_mac64
$MacBook:~ $ /private/tmp/com.apple.launchd.VyYrIR4oEV/org.macosforge.xquartz:0: X IO error.
uim-candwin-gtk: Fatal IO error 35 (Resource temporarily unavailable) on X server /private/tmp/com.apple.launchd.VyYrIR4oEV/org.macosforge.xquartz:0.

代替のPCでしばらく使ってみたところ。問題なく使用できました。
しかし、メインPC以外の２台のPCは、廃棄予定のものであり、
なんとかメインPCの問題を解決したく存じます。

お手数をおかけいたします。
どうぞよろしくお願いいたします。

こんにちは、樋口です。書き込みありがとうございます。

1) うーん，XQuartzは正常に起動しますか？　「アプリケーション」「ユーテ
ィリティ」「XQuartz」をダブルクリックして，「Xterm」というWindowが開け
ばXQuartzが正常に起動したということです。こうなりますでしょうか。

2）インストール時だけでなく，起動時にもセキュリティソフトを切った状態
にしていただくといかがでしょうか？

それでもエラーがになる場合は，コンソールの出力全体を見せていただきます
か？　KH Coder起動時には以下のような表示が出ると思います。ここから下，
最後までです。

bash -c " cd "/Users/k/Downloads/khcoder3/";export LANG=ja_JP.UTF-8;export LC_ALL=ja_JP.UTF-8;export XMODIFIERS="@im=uim";export GTK_IM_MODULE=uim;export DYLD_FALLBACK_LIBRARY_PATH="/Users/k/Downloads/khcoder3/deps/mysql-5.6.17/lib";./x_mac64 "

3）問題なく動く機械と，動かない機械の違いは何でしょうか。インストール
なさっているソフトの違いなど，何か思い当たる点はありますか？　もし何か
あればお知らせください。

樋口先生、こんにちは。
お返事をいただきありがとうございます。
返信が遅くなり失礼いたしました。

1)XQuartzは正常に起動します。「アプリケーション」にある「XQuartz」をダブルクリックすると、「Xterm」というWindowが開きます。
なお、３台ともトラブルが起きていた時に、同様の操作でXQuartzの起動をチェックし、正常な起動を確認いたしました（トラブル報告の際にXQuartzは正常であることについて記載すべきでした。失礼いたしました）

2）インストール時だけでなく，起動時にもセキュリティソフトを切った状態で試してみました。しかし、kh Coderは正常に起動しませんでした。下部にコンソールの出力全体を貼付いたします。
出力は２種類あります。１つめがインストール直後で、２つめが再起動後です（プロジェクト読み込み時に落ちたあとのものです）。

3）問題なく動く機械と，動かない機械を比較します。
問題なく動く機械は２台とも５年以上前のiMacとMacbook Airで、
動かない機械が最も新しく、今年6月に購入したMacbook(2017)です。

動かない機械にインストールした非標準アプリは、下記が全てです。
・AdobeのAcrobat DC、Dreamweaver、Illustrator、Photoshop、Creative Cloud
・Google日本語入力
・eset
・Dropbox
・Microsoft OneDrive
・Microsoft Office（Word、Excel、PowerPoint、OneNote、Outlook）

インストールしているアプリの数は、問題なく動く機械のほうが多いです。
問題なく動く機械には、上記に加えてLine、SlackなどのSNSアプリや、Live safe(マカフィー）、Ingtegoなどのセキュリティソフトや、SPSSも入っています。

あまり役に立たない情報かもしれませんが、
動かない機械のほうで「新規ユーザーアカウント」を作成し、真っ先にkhCoderのインストールを試してみましたが、うまくいきませんでした（コンソール出力は、その際に得られたものです）。
セキュリティソフトを切った状態で試しました。

問題なく動く機械と，動かない機械の違いを考えているのですが、
動かない機械のほうが、まだ色々と触っておらず、購入時の状態に近いです。
すみません…。どうぞよろしくお願いいたします。

----（インストール直後のコンソール出力です）-----

Perl/Tk: 804.032
Resetting parameters...
Locale: ja_JP.UTF-8
This is KH Coder 3.Alpha.13g on darwin.
CWD: /Users/A/Downloads/khcoder3
Executing Mac OS X 64-bit Package
Checking MySQL connection...
Starting MySQL...
uim <-> XIM bridge. Supporting multiple locales.
Using full-synchronous XIM event flow
2018-10-29 23:09:23 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2018-10-29 23:09:23 608 [Warning] Setting lower_case_table_names=2 because file system for /Users/A/Downloads/khcoder3/deps/mysql-5.6.17/data/ is case insensitive
2018-10-29 23:09:23 608 [Note] Plugin 'FEDERATED' is disabled.
2018-10-29 23:09:23 608 [Note] InnoDB: Using atomics to ref count buffer pool pages
2018-10-29 23:09:23 608 [Note] InnoDB: The InnoDB memory heap is disabled
2018-10-29 23:09:23 608 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2018-10-29 23:09:23 608 [Note] InnoDB: Compressed tables use zlib 1.2.3
2018-10-29 23:09:23 608 [Note] InnoDB: Using CPU crc32 instructions
2018-10-29 23:09:23 608 [Note] InnoDB: Initializing buffer pool, size = 512.0M
2018-10-29 23:09:23 608 [Note] InnoDB: Completed initialization of buffer pool
2018-10-29 23:09:23 608 [Note] InnoDB: Highest supported file format is Barracuda.
2018-10-29 23:09:23 608 [Note] InnoDB: The log sequence numbers 76030534 and 76030534 in ibdata files do not match the log sequence number 76193530 in the ib_logfiles!
2018-10-29 23:09:23 608 [Note] InnoDB: Database was not shutdown normally!
2018-10-29 23:09:23 608 [Note] InnoDB: Starting crash recovery.
2018-10-29 23:09:23 608 [Note] InnoDB: Reading tablespace information from the .ibd files...
2018-10-29 23:09:23 608 [Note] InnoDB: Restoring possible half-written data pages
2018-10-29 23:09:23 608 [Note] InnoDB: from the doublewrite buffer...
2018-10-29 23:09:23 608 [Warning] InnoDB: Resizing redo log from 2*3072 to 2*32768 pages, LSN=76193530
2018-10-29 23:09:23 608 [Warning] InnoDB: Starting to delete and rewrite log files.
2018-10-29 23:09:23 608 [Note] InnoDB: Setting log file ./ib_logfile101 size to 512 MB
InnoDB: Progress in MB: 100 200 300 400 500
2018-10-29 23:09:24 608 [Note] InnoDB: Setting log file ./ib_logfile1 size to 512 MB
InnoDB: Progress in MB: 100 200 300 400 500
2018-10-29 23:09:24 608 [Note] InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
2018-10-29 23:09:24 608 [Warning] InnoDB: New log files created, LSN=76193530
2018-10-29 23:09:24 608 [Note] InnoDB: 128 rollback segment(s) are active.
2018-10-29 23:09:24 608 [Note] InnoDB: Waiting for purge to start
2018-10-29 23:09:24 608 [Note] InnoDB: 5.6.17 started; log sequence number 76193530
2018-10-29 23:09:24 608 [Note] Server hostname (bind-address): '*'; port: 3309
2018-10-29 23:09:24 608 [Note] IPv6 is available.
2018-10-29 23:09:24 608 [Note] - '::' resolves to '::';
2018-10-29 23:09:24 608 [Note] Server socket created on IP: '::'.
2018-10-29 23:09:24 608 [Note] Event Scheduler: Loaded 0 events
2018-10-29 23:09:24 608 [Note] deps/MySQL-5.6.17/bin/mysqld: ready for connections.
Version: '5.6.17' socket: '/tmp/mysql.sock.khc3' port: 3309 MySQL Community Server (GPL)
Supported conversion engines:
direct (*)
yahoo-jp (ja)
baidu-olime-jp (ja)
google-cgiapi-jp (ja)
social-ime (ja)
ajax-ime (ja)
look ()
ipa-x-sampa ()
viqr (vi)
pinyin-big5 (zh_TW:zh_HK)
pyunihan (zh)
py (zh_CN)
wb86 (zh_CN:zh_TW:zh_HK)
zm (zh_CN:zh_TW:zh_HK)
m17n-am-sera (am)
m17n-ar-kbd (ar)
m17n-as-inscript (as)
m17n-as-itrans (as)
m17n-as-phonetic (as)
m17n-ath-phonetic (ath)
m17n-be-kbd (be)
m17n-bla-phonetic (bla)
m17n-bn-inscript (bn)
m17n-bn-itrans (bn)
m17n-bn-probhat (bn)
m17n-bn-unijoy (bn)
m17n-bo-ewts (bo)
m17n-bo-tcrc (bo)
m17n-bo-wylie (bo)
m17n-latn-post (*)
m17n-latn-pre (*)
m17n-rfc1345 (*)
m17n-syrc-phonetic (*)
m17n-unicode (*)
m17n-cmc-kbd (cmc)
m17n-cr-western (cr)
m17n-cs-kbd (cs)
m17n-da-post (da)
m17n-dv-phonetic (dv)
m17n-el-kbd (el)
m17n-eo-h-fundamente (eo)
m17n-eo-h-sistemo (eo)
m17n-eo-plena (eo)
m17n-eo-q-sistemo (eo)
m17n-eo-vi-sistemo (eo)
m17n-eo-x-sistemo (eo)
m17n-fa-isiri (fa)
m17n-fr-azerty (fr)
m17n-grc-mizuochi (grc)
m17n-gu-inscript (gu)
m17n-gu-itrans (gu)
m17n-gu-phonetic (gu)
m17n-he-kbd (he)
m17n-hi-inscript (hi)
m17n-hi-itrans (hi)
m17n-hi-phonetic (hi)
m17n-hi-remington (hi)
m17n-hi-typewriter (hi)
m17n-hi-vedmata (hi)
m17n-hr-kbd (hr)
m17n-hy-kbd (hy)
m17n-ii-phonetic (ii)
m17n-en-ispell (en)
m17n-iu-phonetic (iu)
m17n-ja-anthy (ja)
m17n-ja-tcode (ja)
m17n-ja-trycode (ja)
m17n-ka-kbd (ka)
m17n-kk-arabic (kk)
m17n-kk-kbd (kk)
m17n-km-yannis (km)
m17n-kn-inscript (kn)
m17n-kn-itrans (kn)
m17n-kn-kgp (kn)
m17n-ko-han2 (ko)
m17n-ko-romaja (ko)
m17n-ks-inscript (ks)
m17n-ks-kbd (ks)
m17n-lo-kbd (lo)
m17n-lo-lrt (lo)
m17n-ml-inscript (ml)
m17n-ml-itrans (ml)
m17n-ml-mozhi (ml)
m17n-ml-swanalekha (ml)
m17n-mr-inscript (mr)
m17n-mr-itrans (mr)
m17n-mr-phonetic (mr)
m17n-my-kbd (my)
m17n-ne-rom (ne)
m17n-ne-trad (ne)
m17n-nsk-phonetic (nsk)
m17n-oj-phonetic (oj)
m17n-or-inscript (or)
m17n-or-itrans (or)
m17n-or-phonetic (or)
m17n-pa-inscript (pa)
m17n-pa-itrans (pa)
m17n-pa-jhelum (pa)
m17n-pa-phonetic (pa)
m17n-ps-phonetic (ps)
m17n-ru-kbd (ru)
m17n-ru-phonetic (ru)
m17n-ru-translit (ru)
m17n-ru-yawerty (ru)
m17n-sa-harvard-kyoto (sa)
m17n-sa-IAST (sa)
m17n-sd-inscript (sd)
m17n-si-phonetic-dynamic (si)
m17n-si-samanala (si)
m17n-si-singlish (si)
m17n-si-sumihiri (si)
m17n-si-transliteration (si)
m17n-si-wijesekera (si)
m17n-sk-kbd (sk)
m17n-sr-kbd (sr)
m17n-sv-post (sv)
m17n-ta-inscript (ta)
m17n-ta-itrans (ta)
m17n-ta-lk-renganathan (ta)
m17n-ta-phonetic (ta)
m17n-ta-tamil99 (ta)
m17n-ta-typewriter (ta)
m17n-ta-vutam (ta)
m17n-tai-sonla-kbd (tai)
m17n-te-apple (te)
m17n-te-inscript (te)
m17n-te-itrans (te)
m17n-te-pothana (te)
m17n-te-rts (te)
m17n-th-kesmanee (th)
m17n-th-pattachote (th)
m17n-th-tis820 (th)
m17n-ua-kbd (ua)
m17n-ug-kbd (ug)
m17n-ur-phonetic (ur)
m17n-uz-kbd (uz)
m17n-vi-han (vi)
m17n-vi-nomvni (vi)
m17n-vi-nomtelex (vi)
m17n-vi-tcvn (vi)
m17n-vi-telex (vi)
m17n-vi-viqr (vi)
m17n-vi-vni (vi)
m17n-yi-yivo (yi)
m17n-zh-bopomofo (zh)
m17n-zh-cangjie (zh)
m17n-zh-pinyin-vi (zh)
m17n-zh-pinyin (zh)
m17n-zh-py-b5 (zh)
m17n-zh-py-gb (zh)
m17n-zh-py (zh)
m17n-zh-quick (zh)
m17n-zh-tonepy-b5 (zh)
m17n-zh-tonepy-gb (zh)
m17n-zh-tonepy (zh)
elatin ()
latin ()
byeoru (ko)
tutcode (ja)
skk (ja)
prime (ja)
anthy-utf8 (ja)
anthy (ja)
mozc (ja)
XMODIFIERS=@im=uim registered, selecting anthy (ja) as default conversion engine
R Version: 3.1, x86_64
Using un-threaded functions...
Conv:
1 wallclock secs ( 0.46 usr + 0.02 sys = 0.48 CPU)
creating project list... ok
x_mac64(593,0x7fff8f139380) malloc: *** error for object 0x7ffeefbfdf50: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
bash: line 1: 593 Abort trap: 6 ./x_mac64
AnoMacBook:~ A$ /private/tmp/com.apple.launchd.VyYrIR4oEV/org.macosforge.xquartz:0: X IO error.
uim-candwin-gtk: Fatal IO error 35 (Resource temporarily unavailable) on X server /private/tmp/com.apple.launchd.VyYrIR4oEV/org.macosforge.xquartz:0.



----（以下、再起動後のコンソール出力です）-----

Perl/Tk: 804.032
Locale: ja_JP.UTF-8
This is KH Coder 3.Alpha.13g on darwin.
CWD: /Users/A/Downloads/khcoder3
Executing Mac OS X 64-bit Package
Checking MySQL connection...
Starting MySQL...
uim <-> XIM bridge. Supporting multiple locales.
Using full-synchronous XIM event flow
2018-10-30 17:50:23 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2018-10-30 17:50:23 1456 [Warning] Setting lower_case_table_names=2 because file system for /Users/A/Downloads/khcoder3/deps/mysql-5.6.17/data/ is case insensitive
2018-10-30 17:50:23 1456 [Note] Plugin 'FEDERATED' is disabled.
2018-10-30 17:50:23 1456 [Note] InnoDB: Using atomics to ref count buffer pool pages
2018-10-30 17:50:23 1456 [Note] InnoDB: The InnoDB memory heap is disabled
2018-10-30 17:50:23 1456 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2018-10-30 17:50:23 1456 [Note] InnoDB: Compressed tables use zlib 1.2.3
2018-10-30 17:50:23 1456 [Note] InnoDB: Using CPU crc32 instructions
2018-10-30 17:50:23 1456 [Note] InnoDB: Initializing buffer pool, size = 512.0M
2018-10-30 17:50:23 1456 [Note] InnoDB: Completed initialization of buffer pool
2018-10-30 17:50:23 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:23 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:23 1456 [Note] InnoDB: Retrying to lock the first data file
2018-10-30 17:50:24 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:24 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:25 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:25 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:26 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:26 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:27 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:27 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
Supported conversion engines:
direct (*)
yahoo-jp (ja)
baidu-olime-jp (ja)
google-cgiapi-jp (ja)
social-ime (ja)
ajax-ime (ja)
look ()
ipa-x-sampa ()
viqr (vi)
pinyin-big5 (zh_TW:zh_HK)
pyunihan (zh)
py (zh_CN)
wb86 (zh_CN:zh_TW:zh_HK)
zm (zh_CN:zh_TW:zh_HK)
m17n-am-sera (am)
m17n-ar-kbd (ar)
m17n-as-inscript (as)
m17n-as-itrans (as)
m17n-as-phonetic (as)
m17n-ath-phonetic (ath)
m17n-be-kbd (be)
m17n-bla-phonetic (bla)
m17n-bn-inscript (bn)
m17n-bn-itrans (bn)
m17n-bn-probhat (bn)
m17n-bn-unijoy (bn)
m17n-bo-ewts (bo)
m17n-bo-tcrc (bo)
m17n-bo-wylie (bo)
m17n-latn-post (*)
m17n-latn-pre (*)
m17n-rfc1345 (*)
m17n-syrc-phonetic (*)
m17n-unicode (*)
m17n-cmc-kbd (cmc)
m17n-cr-western (cr)
m17n-cs-kbd (cs)
m17n-da-post (da)
m17n-dv-phonetic (dv)
m17n-el-kbd (el)
m17n-eo-h-fundamente (eo)
m17n-eo-h-sistemo (eo)
m17n-eo-plena (eo)
m17n-eo-q-sistemo (eo)
m17n-eo-vi-sistemo (eo)
m17n-eo-x-sistemo (eo)
m17n-fa-isiri (fa)
m17n-fr-azerty (fr)
m17n-grc-mizuochi (grc)
m17n-gu-inscript (gu)
m17n-gu-itrans (gu)
m17n-gu-phonetic (gu)
m17n-he-kbd (he)
m17n-hi-inscript (hi)
m17n-hi-itrans (hi)
m17n-hi-phonetic (hi)
m17n-hi-remington (hi)
m17n-hi-typewriter (hi)
m17n-hi-vedmata (hi)
m17n-hr-kbd (hr)
m17n-hy-kbd (hy)
m17n-ii-phonetic (ii)
m17n-en-ispell (en)
m17n-iu-phonetic (iu)
m17n-ja-anthy (ja)
m17n-ja-tcode (ja)
m17n-ja-trycode (ja)
m17n-ka-kbd (ka)
m17n-kk-arabic (kk)
m17n-kk-kbd (kk)
m17n-km-yannis (km)
m17n-kn-inscript (kn)
m17n-kn-itrans (kn)
m17n-kn-kgp (kn)
m17n-ko-han2 (ko)
m17n-ko-romaja (ko)
m17n-ks-inscript (ks)
m17n-ks-kbd (ks)
m17n-lo-kbd (lo)
m17n-lo-lrt (lo)
m17n-ml-inscript (ml)
m17n-ml-itrans (ml)
m17n-ml-mozhi (ml)
m17n-ml-swanalekha (ml)
m17n-mr-inscript (mr)
m17n-mr-itrans (mr)
m17n-mr-phonetic (mr)
m17n-my-kbd (my)
m17n-ne-rom (ne)
m17n-ne-trad (ne)
m17n-nsk-phonetic (nsk)
m17n-oj-phonetic (oj)
m17n-or-inscript (or)
m17n-or-itrans (or)
m17n-or-phonetic (or)
m17n-pa-inscript (pa)
m17n-pa-itrans (pa)
m17n-pa-jhelum (pa)
m17n-pa-phonetic (pa)
m17n-ps-phonetic (ps)
m17n-ru-kbd (ru)
m17n-ru-phonetic (ru)
m17n-ru-translit (ru)
m17n-ru-yawerty (ru)
m17n-sa-harvard-kyoto (sa)
m17n-sa-IAST (sa)
m17n-sd-inscript (sd)
m17n-si-phonetic-dynamic (si)
m17n-si-samanala (si)
m17n-si-singlish (si)
m17n-si-sumihiri (si)
m17n-si-transliteration (si)
m17n-si-wijesekera (si)
m17n-sk-kbd (sk)
m17n-sr-kbd (sr)
m17n-sv-post (sv)
m17n-ta-inscript (ta)
m17n-ta-itrans (ta)
m17n-ta-lk-renganathan (ta)
m17n-ta-phonetic (ta)
m17n-ta-tamil99 (ta)
m17n-ta-typewriter (ta)
m17n-ta-vutam (ta)
m17n-tai-sonla-kbd (tai)
m17n-te-apple (te)
m17n-te-inscript (te)
m17n-te-itrans (te)
m17n-te-pothana (te)
m17n-te-rts (te)
m17n-th-kesmanee (th)
m17n-th-pattachote (th)
m17n-th-tis820 (th)
m17n-ua-kbd (ua)
m17n-ug-kbd (ug)
m17n-ur-phonetic (ur)
m17n-uz-kbd (uz)
m17n-vi-han (vi)
m17n-vi-nomvni (vi)
m17n-vi-nomtelex (vi)
m17n-vi-tcvn (vi)
m17n-vi-telex (vi)
m17n-vi-viqr (vi)
m17n-vi-vni (vi)
m17n-yi-yivo (yi)
m17n-zh-bopomofo (zh)
m17n-zh-cangjie (zh)
m17n-zh-pinyin-vi (zh)
m17n-zh-pinyin (zh)
m17n-zh-py-b5 (zh)
m17n-zh-py-gb (zh)
m17n-zh-py (zh)
m17n-zh-quick (zh)
m17n-zh-tonepy-b5 (zh)
m17n-zh-tonepy-gb (zh)
m17n-zh-tonepy (zh)
elatin ()
latin ()
byeoru (ko)
tutcode (ja)
skk (ja)
prime (ja)
anthy-utf8 (ja)
anthy (ja)
mozc (ja)
2018-10-30 17:50:28 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:28 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
XMODIFIERS=@im=uim registered, selecting anthy (ja) as default conversion engine
2018-10-30 17:50:29 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:29 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
R Version: 3.1, x86_64
Using un-threaded functions...
2018-10-30 17:50:30 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:30 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:31 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:31 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:32 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:32 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:33 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:33 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:34 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:34 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:35 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:35 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:36 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:36 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:37 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:37 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:38 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:38 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:39 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:39 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:40 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:40 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:41 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:41 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:42 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:42 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:43 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:43 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:44 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:44 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:45 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:45 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:46 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:46 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:47 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:47 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:48 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:48 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:49 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:49 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:50 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:50 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:51 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:51 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:52 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:52 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:53 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:53 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:54 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:54 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:55 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:55 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:56 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:56 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:57 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:57 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:58 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:58 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:50:59 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:50:59 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:00 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:00 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:01 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:01 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:02 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:02 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:03 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:03 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:04 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:04 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:05 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:05 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:06 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:06 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:07 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:07 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:08 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:08 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:09 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:09 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:10 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:10 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:11 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:11 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:12 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:12 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:13 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:13 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:14 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:14 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:15 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:15 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:16 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:16 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:17 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:17 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:18 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:18 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:19 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:19 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:20 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:20 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:21 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:21 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:22 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:22 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:23 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:23 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:24 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:24 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:25 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:25 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:26 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:26 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:27 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:27 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:28 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:28 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:29 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:29 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:30 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:30 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:31 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:31 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:32 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:32 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:33 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:33 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:34 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:34 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:35 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:35 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:36 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:36 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:37 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:37 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:38 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:38 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:39 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:39 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:40 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:40 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:41 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:41 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:42 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:42 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:43 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:43 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:44 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:44 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:45 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:45 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:46 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:46 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:47 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:47 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:48 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:48 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:49 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:49 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:50 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:50 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:51 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:51 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:52 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:52 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:53 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:53 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:54 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:54 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:55 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:55 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:56 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:56 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:57 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:57 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:58 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:58 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:51:59 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:51:59 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:52:00 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:52:00 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:52:01 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:52:01 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:52:02 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:52:02 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:52:03 1456 [ERROR] InnoDB: Unable to lock ./ibdata1, error: 35
2018-10-30 17:52:03 1456 [Note] InnoDB: Check that you do not already have another mysqld process using the same InnoDB data or log files.
2018-10-30 17:52:03 1456 [Note] InnoDB: Unable to open the first data file
2018-10-30 17:52:03 7fff8f139380 InnoDB: Operating system error number 35 in a file operation.
InnoDB: Error number 35 means 'Resource temporarily unavailable'.
InnoDB: Some operating system error numbers are described at
InnoDB: http://dev.mysql.com/doc/refman/5.6/en/operating-system-error-codes.html
2018-10-30 17:52:03 1456 [ERROR] InnoDB: Can't open './ibdata1'
2018-10-30 17:52:03 1456 [ERROR] InnoDB: Could not open or create the system tablespace. If you tried to add new data files to the system tablespace, and it failed here, you should now edit innodb_data_file_path in my.cnf back to what it was, and remove the new ibdata files InnoDB created in this failed attempt. InnoDB only wrote those files full of zeros, but did not yet use them in any way. But be careful: do not remove old data files which contain your precious data!
2018-10-30 17:52:03 1456 [ERROR] Plugin 'InnoDB' init function returned error.
2018-10-30 17:52:03 1456 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2018-10-30 17:52:03 1456 [ERROR] Unknown/unsupported storage engine: InnoDB
2018-10-30 17:52:03 1456 [ERROR] Aborting

2018-10-30 17:52:03 1456 [Note] Binlog end
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'partition'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_METRICS'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_CMPMEM'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_CMP'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_LOCKS'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'INNODB_TRX'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'BLACKHOLE'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'ARCHIVE'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'MRG_MYISAM'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'MyISAM'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'MEMORY'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'CSV'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'sha256_password'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'mysql_old_password'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'mysql_native_password'
2018-10-30 17:52:03 1456 [Note] Shutting down plugin 'binlog'
2018-10-30 17:52:03 1456 [Note] deps/MySQL-5.6.17/bin/mysqld: Shutdown complete

x_mac64(1444,0x7fff8f139380) malloc: *** error for object 0x7ffeefbfdf50: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
bash: line 1: 1444 Abort trap: 6 ./x_mac64
AnoMacBook:~ A$

こんにちは、樋口です。書き込みありがとうございます。

解凍直後にKH Coderがエラーで終了してしまった際，MySQLは動き続けていま
した。本来KH Coderは自分が終了する際にMySQLをShutdownするのですが，こ
れをできないまま落ちてしまっています。

この状態でMacを再起動なさった結果，MySQLのデータベースが壊れて，再起動
後はInnoDB（=MySQL）エラーが出るようになってしまっています。再びInnoDB
（=MySQL）エラー対策が必要な状態に戻ったという状況です。

※Macの再起動前に，もう一度KH Coderを起動し，何もせずに終了すれば，
MySQLがShutdownして，この状況には至らなかったものと思います。

というわけで，ひとまず以下の手順で対策とご確認をお願いできますでしょう
か。以下の手順では再インストールに加えて，速いけれど壊れやすいInnoDBを
やめてMyISAMに変更しています。以下が上手くいけば，そう簡単にはMySQLエ
ラーにはもどらなくなるはずです。

--------------------------------------------------------------------------
1. 「ダウンロード」フォルダの「khcoder3」を削除してください。
2. 画面左上隅のリンゴマークからMacを再起動してください。
3. セキュリティ系ソフトを一時的に無効してから，
4. 再度KH Coderの自動設定ソフトウェアをダウンロード・解凍してください。
5. dep/mysql-5.6.17/khc.cnfをテキストエディタで開き，末尾に以下の3行
　を追加して上書き保存してください

default-storage-engine=MyISAM
default-tmp-storage-engine=MyISAM
skip-innodb

6. 「setup」「kh_coder」を順にクリックしてKH Coderの起動を確認する
　とともに，ターミナルにInnoDBエラーが出ていないことを確認してください。
7. KH Coderをいったん終了してください。
---------------------------------------------------------------------------

ここまで問題なければ，次はmallocエラー対策です。

前回貼り付けていただいたターミナル出力からすると，MySQLを操作しようと
するとmallocエラーになるようです。

一度，InnoDBをやめてMyISAMにした効果がでないか見るということで，新規
プロジェクトを作成してみるのかなと思います。

あとは，MySQLへのアクセスはTCP/IPを使っていますので，ネットワーク接続
を制限するような（ファアーウォール）系のソフトは動いていますでしょうか。
もしそういうものが動いていれば，一時的に無効にしてお試しいただくと良い
かもしれません。

それから，もしもDropboxのような同期ソフトで，ダウンロード・フォルダを
同期している場合には，一時的に同期を止めてお試し下さい。

樋口先生、こんばんは。
ご返信ありがとうございます。

理屈を教えていただき、素人ながら現象を順序立てて整理できるようになってまいりました。
誠にありがとうございます。

明日はどうしても私がお返事できる環境にないため、明後日に、早速試した結果をご報告いたします。

樋口先生、こんばんは。
お返事が遅くなり、失礼いたしました。

再インストールを２度試してみました。
しかし、残念ながら、解決していません。

現在、KH-Coderは問題なく起動します。しかし、プロジェクトを作成できません。
参照先を指定して、プロジェクトを作成しようと「OK」ボタンを押下すると、
ボタンが押されたままの状態でフリーズし、数分して落ちます。

再インストールは、下記の手順で行いました。

（事前の準備：古いkhcoderを一度起動させ、何もせずに終了する）
1. 「ダウンロード」フォルダの「khcoder3」を削除、ゴミ箱を空にする。
2. 画面左上隅のリンゴマークからMacを再起動
3. セキュリティ系ソフト（eset）を一時的に無効にする
4. Macのファイアウォールをオフにする
5. 同期ソフトを全て終了させて同期をオフにする
6. KH Coderの自動設定ソフトウェアをダウンロード・解凍する
7. dep/mysql-5.6.17/khc.cnfをテキストエディタで開き，末尾に以下の3行
　を追加して上書き保存

default-storage-engine=MyISAM
default-tmp-storage-engine=MyISAM
skip-innodb

8. 「setup」「kh_coder」を順にクリックしてKH Coderの起動を確認
9. ターミナルにInnoDBエラーが出ていないことを確認
10. チュートリアルの「kokoro」を参照して、新規プロジェクト→OKボタン

ステップ10まで問題なく進みます。
その後、フリーズして落ちます。

気になる点としては、問題なく作動する他のMacで試した時と比べて起動が遅く、
「Checking MySQL connection...」が表示されたところで何分も止まってしまうことです。
この現象は繰り返し生じます。


以下に、コンソールの出力を貼付いたします。
あまり役立つ情報がなく申し訳ないです…。

Last login: Thu Nov 1 19:29:51 on ttys000
bash -c " cd "/Users/A/Downloads/khcoder3/";export LANG=ja_JP.UTF-8;export LC_ALL=ja_JP.UTF-8;export XMODIFIERS="@im=uim";export GTK_IM_MODULE=uim;export DYLD_FALLBACK_LIBRARY_PATH="/Users/A/Downloads/khcoder3/deps/mysql-5.6.17/lib";./x_mac64"
AnoMacBook:~ A$ bash -c " cd "/Users/A/Downloads/khcoder3/";export LANG=ja_JP.UTF-8;export LC_ALL=ja_JP.UTF-8;export XMODIFIERS="@im=uim";export GTK_IM_MODULE=uim;export DYLD_FALLBACK_LIBRARY_PATH="/Users/A/Downloads/khcoder3/deps/mysql-5.6.17/lib";./x_mac64"
Perl/Tk: 804.032
Resetting parameters...
Locale: ja_JP.UTF-8
This is KH Coder 3.Alpha.13g on darwin.
CWD: /Users/A/Downloads/khcoder3
Executing Mac OS X 64-bit Package
Checking MySQL connection...
Starting MySQL...
uim <-> XIM bridge. Supporting multiple locales.
Using full-synchronous XIM event flow
2018-11-01 19:31:15 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2018-11-01 19:31:15 722 [Warning] Setting lower_case_table_names=2 because file system for /Users/A/Downloads/khcoder3/deps/mysql-5.6.17/data/ is case insensitive
2018-11-01 19:31:15 722 [Note] Plugin 'FEDERATED' is disabled.
2018-11-01 19:31:15 722 [Note] Plugin 'InnoDB' is disabled.
2018-11-01 19:31:15 722 [Note] Server hostname (bind-address): '*'; port: 3309
2018-11-01 19:31:15 722 [Note] IPv6 is available.
2018-11-01 19:31:15 722 [Note] - '::' resolves to '::';
2018-11-01 19:31:15 722 [Note] Server socket created on IP: '::'.
2018-11-01 19:31:15 722 [Warning] Info table is not ready to be used. Table 'mysql.slave_master_info' cannot be opened.
2018-11-01 19:31:15 722 [Warning] Info table is not ready to be used. Table 'mysql.slave_relay_log_info' cannot be opened.
2018-11-01 19:31:15 722 [Note] Event Scheduler: Loaded 0 events
2018-11-01 19:31:15 722 [Note] deps/MySQL-5.6.17/bin/mysqld: ready for connections.
Version: '5.6.17' socket: '/tmp/mysql.sock.khc3' port: 3309 MySQL Community Server (GPL)
Supported conversion engines:
direct (*)
yahoo-jp (ja)
baidu-olime-jp (ja)
google-cgiapi-jp (ja)
social-ime (ja)
ajax-ime (ja)
look ()
ipa-x-sampa ()
viqr (vi)
pinyin-big5 (zh_TW:zh_HK)
pyunihan (zh)
py (zh_CN)
wb86 (zh_CN:zh_TW:zh_HK)
zm (zh_CN:zh_TW:zh_HK)
m17n-am-sera (am)
m17n-ar-kbd (ar)
m17n-as-inscript (as)
m17n-as-itrans (as)
m17n-as-phonetic (as)
m17n-ath-phonetic (ath)
m17n-be-kbd (be)
m17n-bla-phonetic (bla)
m17n-bn-inscript (bn)
m17n-bn-itrans (bn)
m17n-bn-probhat (bn)
m17n-bn-unijoy (bn)
m17n-bo-ewts (bo)
m17n-bo-tcrc (bo)
m17n-bo-wylie (bo)
m17n-latn-post (*)
m17n-latn-pre (*)
m17n-rfc1345 (*)
m17n-syrc-phonetic (*)
m17n-unicode (*)
m17n-cmc-kbd (cmc)
m17n-cr-western (cr)
m17n-cs-kbd (cs)
m17n-da-post (da)
m17n-dv-phonetic (dv)
m17n-el-kbd (el)
m17n-eo-h-fundamente (eo)
m17n-eo-h-sistemo (eo)
m17n-eo-plena (eo)
m17n-eo-q-sistemo (eo)
m17n-eo-vi-sistemo (eo)
m17n-eo-x-sistemo (eo)
m17n-fa-isiri (fa)
m17n-fr-azerty (fr)
m17n-grc-mizuochi (grc)
m17n-gu-inscript (gu)
m17n-gu-itrans (gu)
m17n-gu-phonetic (gu)
m17n-he-kbd (he)
m17n-hi-inscript (hi)
m17n-hi-itrans (hi)
m17n-hi-phonetic (hi)
m17n-hi-remington (hi)
m17n-hi-typewriter (hi)
m17n-hi-vedmata (hi)
m17n-hr-kbd (hr)
m17n-hy-kbd (hy)
m17n-ii-phonetic (ii)
m17n-en-ispell (en)
m17n-iu-phonetic (iu)
m17n-ja-anthy (ja)
m17n-ja-tcode (ja)
m17n-ja-trycode (ja)
m17n-ka-kbd (ka)
m17n-kk-arabic (kk)
m17n-kk-kbd (kk)
m17n-km-yannis (km)
m17n-kn-inscript (kn)
m17n-kn-itrans (kn)
m17n-kn-kgp (kn)
m17n-ko-han2 (ko)
m17n-ko-romaja (ko)
m17n-ks-inscript (ks)
m17n-ks-kbd (ks)
m17n-lo-kbd (lo)
m17n-lo-lrt (lo)
m17n-ml-inscript (ml)
m17n-ml-itrans (ml)
m17n-ml-mozhi (ml)
m17n-ml-swanalekha (ml)
m17n-mr-inscript (mr)
m17n-mr-itrans (mr)
m17n-mr-phonetic (mr)
m17n-my-kbd (my)
m17n-ne-rom (ne)
m17n-ne-trad (ne)
m17n-nsk-phonetic (nsk)
m17n-oj-phonetic (oj)
m17n-or-inscript (or)
m17n-or-itrans (or)
m17n-or-phonetic (or)
m17n-pa-inscript (pa)
m17n-pa-itrans (pa)
m17n-pa-jhelum (pa)
m17n-pa-phonetic (pa)
m17n-ps-phonetic (ps)
m17n-ru-kbd (ru)
m17n-ru-phonetic (ru)
m17n-ru-translit (ru)
m17n-ru-yawerty (ru)
m17n-sa-harvard-kyoto (sa)
m17n-sa-IAST (sa)
m17n-sd-inscript (sd)
m17n-si-phonetic-dynamic (si)
m17n-si-samanala (si)
m17n-si-singlish (si)
m17n-si-sumihiri (si)
m17n-si-transliteration (si)
m17n-si-wijesekera (si)
m17n-sk-kbd (sk)
m17n-sr-kbd (sr)
m17n-sv-post (sv)
m17n-ta-inscript (ta)
m17n-ta-itrans (ta)
m17n-ta-lk-renganathan (ta)
m17n-ta-phonetic (ta)
m17n-ta-tamil99 (ta)
m17n-ta-typewriter (ta)
m17n-ta-vutam (ta)
m17n-tai-sonla-kbd (tai)
m17n-te-apple (te)
m17n-te-inscript (te)
m17n-te-itrans (te)
m17n-te-pothana (te)
m17n-te-rts (te)
m17n-th-kesmanee (th)
m17n-th-pattachote (th)
m17n-th-tis820 (th)
m17n-ua-kbd (ua)
m17n-ug-kbd (ug)
m17n-ur-phonetic (ur)
m17n-uz-kbd (uz)
m17n-vi-han (vi)
m17n-vi-nomvni (vi)
m17n-vi-nomtelex (vi)
m17n-vi-tcvn (vi)
m17n-vi-telex (vi)
m17n-vi-viqr (vi)
m17n-vi-vni (vi)
m17n-yi-yivo (yi)
m17n-zh-bopomofo (zh)
m17n-zh-cangjie (zh)
m17n-zh-pinyin-vi (zh)
m17n-zh-pinyin (zh)
m17n-zh-py-b5 (zh)
m17n-zh-py-gb (zh)
m17n-zh-py (zh)
m17n-zh-quick (zh)
m17n-zh-tonepy-b5 (zh)
m17n-zh-tonepy-gb (zh)
m17n-zh-tonepy (zh)
elatin ()
latin ()
byeoru (ko)
tutcode (ja)
skk (ja)
prime (ja)
anthy-utf8 (ja)
anthy (ja)
mozc (ja)
XMODIFIERS=@im=uim registered, selecting anthy (ja) as default conversion engine
R Version: 3.1, x86_64
Using un-threaded functions...
creating project list... ok
Conv:
1 wallclock secs ( 0.10 usr + 0.01 sys = 0.11 CPU)
x_mac64(711,0x7fffad602380) malloc: *** error for object 0x7ffeefbfdf50: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
bash: line 1: 711 Abort trap: 6 ./x_mac64


AnoMacBook:~ A$ /private/tmp/com.apple.launchd.7QRrdMiekc/org.macosforge.xquartz:0: X IO error.
uim-candwin-gtk: Fatal IO error 35 (Resource temporarily unavailable) on X server /private/tmp/com.apple.launchd.7QRrdMiekc/org.macosforge.xquartz:0.
=ja_JP.UTF-8;export LC_ALL=ja_JP.UTF-8;export XMODIFIERS="@im=uim";export GTK_IM_MODULE=uim;export DYLD_FALLBACK_LIBRARY_PATH="/Users/A/Downloads/khcoder3/deps/mysql-5.6.17/lib";./x_mac64 "
Perl/Tk: 804.032
Locale: ja_JP.UTF-8
This is KH Coder 3.Alpha.13g on darwin.
CWD: /Users/A/Downloads/khcoder3
Executing Mac OS X 64-bit Package
Checking MySQL connection...
Starting MySQL...
uim <-> XIM bridge. Supporting multiple locales.
Using full-synchronous XIM event flow
2018-11-01 19:35:57 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2018-11-01 19:35:57 925 [Warning] Setting lower_case_table_names=2 because file system for /Users/A/Downloads/khcoder3/deps/mysql-5.6.17/data/ is case insensitive
2018-11-01 19:35:57 925 [Note] Plugin 'FEDERATED' is disabled.
2018-11-01 19:35:57 925 [Note] Plugin 'InnoDB' is disabled.
2018-11-01 19:35:57 925 [Note] Server hostname (bind-address): '*'; port: 3309
2018-11-01 19:35:57 925 [Note] IPv6 is available.
2018-11-01 19:35:57 925 [Note] - '::' resolves to '::';
2018-11-01 19:35:57 925 [Note] Server socket created on IP: '::'.
2018-11-01 19:35:57 925 [ERROR] Can't start server: Bind on TCP/IP port: Address already in use
2018-11-01 19:35:57 925 [ERROR] Do you already have another mysqld server running on port: 3309 ?
2018-11-01 19:35:57 925 [ERROR] Aborting

2018-11-01 19:35:57 925 [Note] Binlog end
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'partition'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_METRICS'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_CMPMEM'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_CMP'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_LOCKS'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'INNODB_TRX'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'BLACKHOLE'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'ARCHIVE'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'MRG_MYISAM'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'MyISAM'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'MEMORY'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'CSV'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'sha256_password'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'mysql_old_password'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'mysql_native_password'
2018-11-01 19:35:57 925 [Note] Shutting down plugin 'binlog'
2018-11-01 19:35:57 925 [Note] deps/MySQL-5.6.17/bin/mysqld: Shutdown complete

sh: line 1: 898 Killed: 9 /Users/A/Downloads/khcoder3/deps/R-3.1.0/Resources/bin/R --slave --vanilla < start.r > output.log
Supported conversion engines:
direct (*)
yahoo-jp (ja)
baidu-olime-jp (ja)
google-cgiapi-jp (ja)
social-ime (ja)
ajax-ime (ja)
look ()
ipa-x-sampa ()
viqr (vi)
pinyin-big5 (zh_TW:zh_HK)
pyunihan (zh)
py (zh_CN)
wb86 (zh_CN:zh_TW:zh_HK)
zm (zh_CN:zh_TW:zh_HK)
m17n-am-sera (am)
m17n-ar-kbd (ar)
m17n-as-inscript (as)
m17n-as-itrans (as)
m17n-as-phonetic (as)
m17n-ath-phonetic (ath)
m17n-be-kbd (be)
m17n-bla-phonetic (bla)
m17n-bn-inscript (bn)
m17n-bn-itrans (bn)
m17n-bn-probhat (bn)
m17n-bn-unijoy (bn)
m17n-bo-ewts (bo)
m17n-bo-tcrc (bo)
m17n-bo-wylie (bo)
m17n-latn-post (*)
m17n-latn-pre (*)
m17n-rfc1345 (*)
m17n-syrc-phonetic (*)
m17n-unicode (*)
m17n-cmc-kbd (cmc)
m17n-cr-western (cr)
m17n-cs-kbd (cs)
m17n-da-post (da)
m17n-dv-phonetic (dv)
m17n-el-kbd (el)
m17n-eo-h-fundamente (eo)
m17n-eo-h-sistemo (eo)
m17n-eo-plena (eo)
m17n-eo-q-sistemo (eo)
m17n-eo-vi-sistemo (eo)
m17n-eo-x-sistemo (eo)
m17n-fa-isiri (fa)
m17n-fr-azerty (fr)
m17n-grc-mizuochi (grc)
m17n-gu-inscript (gu)
m17n-gu-itrans (gu)
m17n-gu-phonetic (gu)
m17n-he-kbd (he)
m17n-hi-inscript (hi)
m17n-hi-itrans (hi)
m17n-hi-phonetic (hi)
m17n-hi-remington (hi)
m17n-hi-typewriter (hi)
m17n-hi-vedmata (hi)
m17n-hr-kbd (hr)
m17n-hy-kbd (hy)
m17n-ii-phonetic (ii)
m17n-en-ispell (en)
m17n-iu-phonetic (iu)
m17n-ja-anthy (ja)
m17n-ja-tcode (ja)
m17n-ja-trycode (ja)
m17n-ka-kbd (ka)
m17n-kk-arabic (kk)
m17n-kk-kbd (kk)
m17n-km-yannis (km)
m17n-kn-inscript (kn)
m17n-kn-itrans (kn)
m17n-kn-kgp (kn)
m17n-ko-han2 (ko)
m17n-ko-romaja (ko)
m17n-ks-inscript (ks)
m17n-ks-kbd (ks)
m17n-lo-kbd (lo)
m17n-lo-lrt (lo)
m17n-ml-inscript (ml)
m17n-ml-itrans (ml)
m17n-ml-mozhi (ml)
m17n-ml-swanalekha (ml)
m17n-mr-inscript (mr)
m17n-mr-itrans (mr)
m17n-mr-phonetic (mr)
m17n-my-kbd (my)
m17n-ne-rom (ne)
m17n-ne-trad (ne)
m17n-nsk-phonetic (nsk)
m17n-oj-phonetic (oj)
m17n-or-inscript (or)
m17n-or-itrans (or)
m17n-or-phonetic (or)
m17n-pa-inscript (pa)
m17n-pa-itrans (pa)
m17n-pa-jhelum (pa)
m17n-pa-phonetic (pa)
m17n-ps-phonetic (ps)
m17n-ru-kbd (ru)
m17n-ru-phonetic (ru)
m17n-ru-translit (ru)
m17n-ru-yawerty (ru)
m17n-sa-harvard-kyoto (sa)
m17n-sa-IAST (sa)
m17n-sd-inscript (sd)
m17n-si-phonetic-dynamic (si)
m17n-si-samanala (si)
m17n-si-singlish (si)
m17n-si-sumihiri (si)
m17n-si-transliteration (si)
m17n-si-wijesekera (si)
m17n-sk-kbd (sk)
m17n-sr-kbd (sr)
m17n-sv-post (sv)
m17n-ta-inscript (ta)
m17n-ta-itrans (ta)
m17n-ta-lk-renganathan (ta)
m17n-ta-phonetic (ta)
m17n-ta-tamil99 (ta)
m17n-ta-typewriter (ta)
m17n-ta-vutam (ta)
m17n-tai-sonla-kbd (tai)
m17n-te-apple (te)
m17n-te-inscript (te)
m17n-te-itrans (te)
m17n-te-pothana (te)
m17n-te-rts (te)
m17n-th-kesmanee (th)
m17n-th-pattachote (th)
m17n-th-tis820 (th)
m17n-ua-kbd (ua)
m17n-ug-kbd (ug)
m17n-ur-phonetic (ur)
m17n-uz-kbd (uz)
m17n-vi-han (vi)
m17n-vi-nomvni (vi)
m17n-vi-nomtelex (vi)
m17n-vi-tcvn (vi)
m17n-vi-telex (vi)
m17n-vi-viqr (vi)
m17n-vi-vni (vi)
m17n-yi-yivo (yi)
m17n-zh-bopomofo (zh)
m17n-zh-cangjie (zh)
m17n-zh-pinyin-vi (zh)
m17n-zh-pinyin (zh)
m17n-zh-py-b5 (zh)
m17n-zh-py-gb (zh)
m17n-zh-py (zh)
m17n-zh-quick (zh)
m17n-zh-tonepy-b5 (zh)
m17n-zh-tonepy-gb (zh)
m17n-zh-tonepy (zh)
elatin ()
latin ()
byeoru (ko)
tutcode (ja)
skk (ja)
prime (ja)
anthy-utf8 (ja)
anthy (ja)
mozc (ja)
XMODIFIERS=@im=uim registered, selecting anthy (ja) as default conversion engine
R Version: 3.1, x86_64
Using un-threaded functions...
Conv:
0 wallclock secs ( 0.28 usr + 0.01 sys = 0.29 CPU)
x_mac64(911,0x7fffad602380) malloc: *** error for object 0x7ffeefbfdf50: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
bash: line 1: 911 Abort trap: 6 ./x_mac64
AnoMacBook:~ A$

こんにちは、樋口です。書き込みありがとうございます。

> 「Checking MySQL connection...」が表示されたところで何分も止まってし
> まうことです。

これは明らかに異常ですね。ここではTCP/IP（ネットワーク）を使ってMySQL
への接続を試行しています。

可能性として考えられることの1つは，やはり，ネットワーク接続を制御する
ような（ファアーウォール系の）ソフトに止められていることでしょうか。
この手のソフトウェア，お使いでしょうか？

もしお使いでしたら，ファイアーウォールやインターネットセキュリティと呼
ばれるようなソフトウェアを，一時的に無効にしてお試しいただくのが一手
かと存じます。


もう1つの可能性としては，MySQLが使おうとしているTCP Port 3309が既に
別のソフトウェアに使われているということも考えられます。KH Coderを
起動する前に，現在どのIPアドレス・ポートが使用中(LISTEN)かをお調べ
いただくといかがでしょう？ 3309が使用中になっていたりしないでしょうか？

調べ方のご参考: https://rensrv.com/macos/ip-address-port-in-use/

こんにちは、樋口です。書き込みありがとうございます。

なにはともあれお疲れさまでした。

今後もし同様のエラーが生じた場合は、
1. KH Coderを終了
2. MySQL（mysqld）を強制終了
3. KH Coderを再び起動する
という手順をお試しいただくとよさそうに思います。再インストールしなく
てもこれで復活する可能性がありそうに思っています。

InnoDBだとMySQL（mysqld）の強制終了時に壊れてしまったりするのですが，
今回InnoDBからMyISAMに変えていますので、強制終了してもそうそう壊れない
からです。

p.s.
今回の件を教訓に、3.Alpha.14bからはデフォルトでMyISAMにいたしました。