デプロイ時にmysql2のインストールができない

Question

前提・実現したいこと

ここに質問の内容を詳しく書いてください。
RailsアプリをVPS(Conoha)で動かすことを目的としています。
デプロイ時にmysql2のインストールの際エラーが出ています。

発生している問題・エラーメッセージ

To see why this extension failed to compile, please check the mkmf.log which can
be found here:

/var/www/portfolio/shared/bundle/ruby/3.0.0/extensions/x86_64-linux/3.0.0/mysql2-0.5.3/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in
/var/www/portfolio/shared/bundle/ruby/3.0.0/gems/mysql2-0.5.3 for inspection.
Results logged to
/var/www/portfolio/shared/bundle/ruby/3.0.0/extensions/x86_64-linux/3.0.0/mysql2-0.5.3/gem_make.out

An error occurred while installing mysql2 (0.5.3), and Bundler cannot
continue.
Make sure that `gem install mysql2 -v '0.5.3' --source 'https://rubygems.org/'`
succeeds before bundling.

In Gemfile:
  mysql2
bundle stderr: Nothing written


** DEPLOY FAILED
** Refer to log/capistrano.log for details. Here are the last 20 lines:




To see why this extension failed to compile, please check the mkmf.log which can

be found here:



/var/www/portfolio/shared/bundle/ruby/3.0.0/extensions/x86_64-linux/3.0.0/mysql2-0.5.3/mkmf.log

該当のソースコード

bundle exec cap production deploy　
上記コマンドでデプロイ実行しています。

試したこと

①エラ〜メッセージ通り、gem install mysql2 -v '0.5.3' --source 'https://rubygems.org/'
を実行してbundle installしましたが改善されませんでした。
②bundle config --local build.mysql2 "--with-ldflags=-L/usr/local/opt/openssl/lib"
コマンドを打ち、bundle installしましたが効果なしでした。
③またGemfileに直接バージョン指定して同じくbundle installしましたが、こちらも効果なしでした。

補足情報（FW/ツールのバージョンなど）

何か不足情報ありましたらご教授ください。
何卒宜しくお願いします。

Answer 1

多分なにかfileが足りないのです。
エラーメッセージに　To see why this extension failed to compile, please check the mkmf.log　
と有るように、そこを読んでください。
何が原因なのかが書かれています。多分どうすればよいかも書かれています。

Comments

[Naoto1]

ありがとうございます。
エラーの読み方に慣れておらず、大変助かりました。
一度見てみます！

[Naoto1]

catコマンドを使用してエラーログを表示させてみました。
‘rb_wait_for_single_fd’ が宣言されていないなどのエラーが出ていたので
調べてみたのですが、理解が乏しく解決には至りませんでした。

知見を貸して頂けると幸甚です。

"gcc -std=gnu99 -o conftest -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/x86_64-linux -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/ruby/backward -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0 -I. -I/home/localadmin/.rbenv/versions/3.0.0/include -O3 -ggdb3 -Wall -Wextra -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wsuggest-attribute=format -Wsuggest-attribute=noreturn -Wunused-variable -fPIC conftest.c -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -fstack-protector-strong -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L/home/localadmin/.rbenv/versions/3.0.0/lib -lruby -lm -lc"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(int argc, char **argv)
4: {
5: return !!argv[argc];
6: }
/* end */

"gcc -std=gnu99 -o conftest -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/x86_64-linux -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/ruby/backward -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0 -I. -I/home/localadmin/.rbenv/versions/3.0.0/include -O3 -ggdb3 -Wall -Wextra -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wsuggest-attribute=format -Wsuggest-attribute=noreturn -Wunused-variable -fPIC conftest.c -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -fstack-protector-strong -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L/home/localadmin/.rbenv/versions/3.0.0/lib -lruby -lm -lc"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: /*top*/
4: extern int t(void);
5: int main(int argc, char **argv)
6: {
7: if (argc > 1000000) {
8: int (* volatile tp)(void)=(int (*)(void))&t;
9: printf("%d", (*tp)());
10: }
11:
12: return !!argv[argc];
13: }
14: int t(void) { void ((*volatile p)()); p = (void ((*)()))rb_absint_size; return !p; }
/* end */

--------------------

have_func: checking for rb_absint_singlebit_p()... -------------------- yes

"gcc -std=gnu99 -o conftest -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/x86_64-linux -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/ruby/backward -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0 -I. -I/home/localadmin/.rbenv/versions/3.0.0/include -O3 -ggdb3 -Wall -Wextra -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wsuggest-attribute=format -Wsuggest-attribute=noreturn -Wunused-variable -fPIC conftest.c -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -fstack-protector-strong -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L/home/localadmin/.rbenv/versions/3.0.0/lib -lruby -lm -lc"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: /*top*/
4: extern int t(void);
5: int main(int argc, char **argv)
6: {
7: if (argc > 1000000) {
8: int (* volatile tp)(void)=(int (*)(void))&t;
9: printf("%d", (*tp)());
10: }
11:
12: return !!argv[argc];
13: }
14: int t(void) { void ((*volatile p)()); p = (void ((*)()))rb_absint_singlebit_p; return !p; }
/* end */

--------------------

have_func: checking for rb_wait_for_single_fd()... -------------------- yes

"gcc -std=gnu99 -o conftest -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/x86_64-linux -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/ruby/backward -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0 -I. -I/home/localadmin/.rbenv/versions/3.0.0/include -O3 -ggdb3 -Wall -Wextra -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wsuggest-attribute=format -Wsuggest-attribute=noreturn -Wunused-variable -fPIC conftest.c -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -fstack-protector-strong -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L/home/localadmin/.rbenv/versions/3.0.0/lib -lruby -lm -lc"
conftest.c: 関数 ‘t’ 内:
conftest.c:14:57: エラー: ‘rb_wait_for_single_fd’ が宣言されていません (この関数内での最初の使用)
int t(void) { void ((*volatile p)()); p = (void ((*)()))rb_wait_for_single_fd; return !p; }
^
conftest.c:14:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
conftest.c: トップレベル:
cc1: 警告: 認識できないコマンドラインオプション "-Wno-tautological-compare" です [デフォルトで有効]
cc1: 警告: 認識できないコマンドラインオプション "-Wno-self-assign" です [デフォルトで有効]
cc1: 警告: 認識できないコマンドラインオプション "-Wno-parentheses-equality" です [デフォルトで有効]
cc1: 警告: 認識できないコマンドラインオプション "-Wno-constant-logical-operand" です [デフォルトで有効]
cc1: 警告: 認識できないコマンドラインオプション "-Wno-cast-function-type" です [デフォルトで有効]
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: /*top*/
4: extern int t(void);
5: int main(int argc, char **argv)
6: {
7: if (argc > 1000000) {
8: int (* volatile tp)(void)=(int (*)(void))&t;
9: printf("%d", (*tp)());
10: }
11:
12: return !!argv[argc];
13: }
14: int t(void) { void ((*volatile p)()); p = (void ((*)()))rb_wait_for_single_fd; return !p; }
/* end */

"gcc -std=gnu99 -o conftest -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/x86_64-linux -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0/ruby/backward -I/home/localadmin/.rbenv/versions/3.0.0/include/ruby-3.0.0 -I. -I/home/localadmin/.rbenv/versions/3.0.0/include -O3 -ggdb3 -Wall -Wextra -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wsuggest-attribute=format -Wsuggest-attribute=noreturn -Wunused-variable -fPIC conftest.c -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L. -L/home/localadmin/.rbenv/versions/3.0.0/lib -fstack-protector-strong -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/localadmin/.rbenv/versions/3.0.0/lib -L/home/localadmin/.rbenv/versions/3.0.0/lib -lruby -lm -lc"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: /*top*/
4: extern int t(void);
5: int main(int argc, char **argv)
6: {
7: if (argc > 1000000) {
8: int (* volatile tp)(void)=(int (*)(void))&t;
9: printf("%d", (*tp)());
10: }
11:
12: return !!argv[argc];
13: }
14: extern void rb_wait_for_single_fd();
15: int t(void) { rb_wait_for_single_fd(); return 0; }
/* end */

[winterboum]

これがlogの最後ですか？

[Naoto1]

上記がlogの最後になります。

他にcapistranoのエラーも出ておりましたのでログを取ってみました。
DEBUG [81de31f3] The following gems are missing
* mysql2 (0.5.3)
Install missing gems with `bundle install`
DEBUG [81de31f3] Finished in 0.467 seconds with exit status 1 (failed).
INFO [7ba341f1] Running RBENV_ROOT=/home/localadmin/.rbenv RBENV_VERSION=3.0.0 /home/localadmin/.rbenv/bin/rbenv exec bundle install --jobs 4 --quiet as localadmin@118.27.9.129
DEBUG [7ba341f1] Command: cd /var/www/portfolio/releases/20210407142316 && ( export RBENV_ROOT="/home/localadmin/.rbenv" RBENV_VERSION="3.0.0" ; RBENV_ROOT=/home/localadmin/.rbenv RBENV_VERSION=3.0.0 /home/localadmin/.rbenv/bin/rbenv exec bundle install --jobs 4 --quiet )
DEBUG [7ba341f1] Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

mysql2はインストール済み（0.5.3)及び、Gemも重複していないのですが
同じログが表示され続けている状態です。。。

[winterboum]

mysql2 のいんsトールが成功していないんだと思いますよ。
mkmf.log　の全体ではなく、最後が重要です。そこは上のlogにでてますか？

[Naoto1]

ご回答ありがとうございます。
すみません。全文送ってませんでした。
DEBUG [e48c1917] Command: cd /var/www/portfolio/releases/20210407233743 && ( export RBENV_ROOT="/home/localadmin/.rbenv" RBENV_VERSION="3.0.0" ; RBENV_ROOT=/home/localadmin/.rbenv RBENV_VERSION=3.0.0 /home/localadmin/.rbenv/bin/rbenv exec bundle config --local path /var/www/portfolio/shared/bundle )
INFO [e48c1917] Finished in 0.358 seconds with exit status 0 (successful).
INFO [57e84a1a] Running RBENV_ROOT=/home/localadmin/.rbenv RBENV_VERSION=3.0.0 /home/localadmin/.rbenv/bin/rbenv exec bundle config --local without development:test as localadmin@118.27.9.129
DEBUG [57e84a1a] Command: cd /var/www/portfolio/releases/20210407233743 && ( export RBENV_ROOT="/home/localadmin/.rbenv" RBENV_VERSION="3.0.0" ; RBENV_ROOT=/home/localadmin/.rbenv RBENV_VERSION=3.0.0 /home/localadmin/.rbenv/bin/rbenv exec bundle config --local without development:test )
INFO [57e84a1a] Finished in 0.364 seconds with exit status 0 (successful).
DEBUG [f5bc21e8] Running if test ! -d /var/www/portfolio/releases/20210407233743; then echo "Directory does not exist '/var/www/portfolio/releases/20210407233743'" 1>&2; false; fi as localadmin@118.27.9.129
DEBUG [f5bc21e8] Command: if test ! -d /var/www/portfolio/releases/20210407233743; then echo "Directory does not exist '/var/www/portfolio/releases/20210407233743'" 1>&2; false; fi
DEBUG [f5bc21e8] Finished in 0.103 seconds with exit status 0 (successful).
DEBUG [d5d3dfdc] Running RBENV_ROOT=/home/localadmin/.rbenv RBENV_VERSION=3.0.0 /home/localadmin/.rbenv/bin/rbenv exec bundle check as localadmin@118.27.9.129
DEBUG [d5d3dfdc] Command: cd /var/www/portfolio/releases/20210407233743 && ( export RBENV_ROOT="/home/localadmin/.rbenv" RBENV_VERSION="3.0.0" ; RBENV_ROOT=/home/localadmin/.rbenv RBENV_VERSION=3.0.0 /home/localadmin/.rbenv/bin/rbenv exec bundle check )
DEBUG [d5d3dfdc] The following gems are missing
* mysql2 (0.5.3)
Install missing gems with `bundle install`
DEBUG [d5d3dfdc] Finished in 0.607 seconds with exit status 1 (failed).
INFO [e57b422c] Running RBENV_ROOT=/home/localadmin/.rbenv RBENV_VERSION=3.0.0 /home/localadmin/.rbenv/bin/rbenv exec bundle install --jobs 4 --quiet as localadmin@118.27.9.129
DEBUG [e57b422c] Command: cd /var/www/portfolio/releases/20210407233743 && ( export RBENV_ROOT="/home/localadmin/.rbenv" RBENV_VERSION="3.0.0" ; RBENV_ROOT=/home/localadmin/.rbenv RBENV_VERSION=3.0.0 /home/localadmin/.rbenv/bin/rbenv exec bundle install --jobs 4 --quiet )
DEBUG [e57b422c] Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

current directory:
/var/www/portfolio/shared/bundle/ruby/3.0.0/gems/mysql2-0.5.3/ext/mysql2
/home/localadmin/.rbenv/versions/3.0.0/bin/ruby -I
/home/localadmin/.rbenv/versions/3.0.0/lib/ruby/site_ruby/3.0.0 -r
./siteconf20210408-27879-bposbq.rb extconf.rb
--with-ldflags\=-L/usr/local/opt/openssl/lib
checking for rb_absint_size()... yes
checking for rb_absint_singlebit_p()... yes
checking for rb_wait_for_single_fd()... yes
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers. Check the mkmf.log file for more details. You may
need configuration options.

Provided configuration options:
--with-opt-dir
--without-opt-dir
--with-opt-include
--without-opt-include=${opt-dir}/include
--with-opt-lib
--without-opt-lib=${opt-dir}/lib
--with-make-prog
--without-make-prog
--srcdir=.
--curdir
--ruby=/home/localadmin/.rbenv/versions/3.0.0/bin/$(RUBY_BASE_NAME)
--with-mysql-dir
--without-mysql-dir
--with-mysql-include
--without-mysql-include=${mysql-dir}/include
--with-mysql-lib
--without-mysql-lib=${mysql-dir}/lib
--with-mysql-config
--without-mysql-config
--with-mysqlclient-dir
--without-mysqlclient-dir
--with-mysqlclient-include
--without-mysqlclient-include=${mysqlclient-dir}/include
--with-mysqlclient-lib
--without-mysqlclient-lib=${mysqlclient-dir}/lib
--with-mysqlclientlib
--without-mysqlclientlib
/home/localadmin/.rbenv/versions/3.0.0/lib/ruby/3.0.0/mkmf.rb:1050:in `block in
find_library': undefined method `split' for nil:NilClass (NoMethodError)
from /home/localadmin/.rbenv/versions/3.0.0/lib/ruby/3.0.0/mkmf.rb:1050:in
`collect'
from /home/localadmin/.rbenv/versions/3.0.0/lib/ruby/3.0.0/mkmf.rb:1050:in
`find_library'
from extconf.rb:87:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can
be found here:

/var/www/portfolio/shared/bundle/ruby/3.0.0/extensions/x86_64-linux/3.0.0/mysql2-0.5.3/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in
/var/www/portfolio/shared/bundle/ruby/3.0.0/gems/mysql2-0.5.3 for inspection.
Results logged to
/var/www/portfolio/shared/bundle/ruby/3.0.0/extensions/x86_64-linux/3.0.0/mysql2-0.5.3/gem_make.out

An error occurred while installing mysql2 (0.5.3), and Bundler cannot
continue.
Make sure that `gem install mysql2 -v '0.5.3' --source 'https://rubygems.org/'`
succeeds before bundling.

In Gemfile:
mysql2
INFO ---------------------------------------------------------------------------
INFO START 2021-04-08 10:33:16 +0900 cap production deploy
INFO ---------------------------------------------------------------------------
DEBUG [b957f79a] Running [ -d /home/localadmin/.rbenv/versions/3.0.0 ] as localadmin@118.27.9.129
DEBUG [b957f79a] Command: [ -d /home/localadmin/.rbenv/versions/3.0.0 ]
DEBUG [b957f79a] Finished in 0.725 seconds with exit status 0 (successful).
INFO [f46ece30] Running /usr/bin/env mkdir -p /tmp as localadmin@118.27.9.129
DEBUG [f46ece30] Command: ( export RBENV_ROOT="/home/localadmin/.rbenv" RBENV_VERSION="3.0.0" ; /usr/bin/env mkdir -p /tmp )
INFO [f46ece30] Finished in 0.097 seconds with exit status 0 (successful).
DEBUG Uploading /tmp/git-ssh-d9323b3d44e8d70692e2.sh 0.0%
INFO Uploading /tmp/git-ssh-d9323b3d44e8d70692e2.sh 100.0%
INFO [8ec512c9] Running /usr/bin/env chmod 700 /tmp/git-ssh-d9323b3d44e8d70692e2.sh as localadmin@118.27.9.129
DEBUG [8ec512c9] Command: ( export RBENV_ROOT="/home/localadmin/.rbenv" RBENV_VERSION="3.0.0" ; /usr/bin/env chmod 700 /tmp/git-ssh-d9323b3d44e8d70692e2.sh )
INFO [8ec512c9] Finished in 0.100 seconds with exit status 0 (successful).
INFO [b7456ee1] Running /usr/bin/env git ls-remote [e-mail]:Naoto3615/portfolio.git HEAD as localadmin@118.27.9.129
DEBUG [b7456ee1] Command: ( export RBENV_ROOT="/home/localadmin/.rbenv" RBENV_VERSION="3.0.0" GIT_ASKPASS="/bin/echo" GIT_SSH="/tmp/git-ssh-d9323b3d44e8d70692e2.sh" ; /usr/bin/env git ls-remote [e-mail]:Naoto3615/portfolio.git HEAD )
DEBUG [b7456ee1] Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

長文で申し訳ないです。
もう一度mysql2のインストールをし直してみます。

[Naoto1]

gem install mysql2 -v '0.5.3' --source 'https://rubygems.org/' -- --with-cppflags=-I/usr/local/opt/openssl/include --with-ldflags=-L/usr/local/opt/openssl/lib
上記コマンドを打ちました。

→→結果
Building native extensions with: '--with-cppflags=-I/usr/local/opt/openssl/include --with-ldflags=-L/usr/local/opt/openssl/lib'
This could take a while...
Successfully installed mysql2-0.5.3
Parsing documentation for mysql2-0.5.3
Done installing documentation for mysql2 after 0 seconds
1 gem installed

インストールはされたような記述が書かれているのですが、デプロイ時には
同じエラーが出現しました。
解決策が見い出せず悩み中です。。。。

[winterboum]

すると、インストール場所が違うのかな。
bundle install ではシステムエリア にいれてます？　それとも Rails.root のvender とかに入れてます？

[Naoto1]

ご回答ありがとうございます。
bundle instal はシステムに入ってました。

[Naoto1]

bundle installすると
Using mysql2 0.5.3の表示があるので
インストールはされているようですが、場所がどこに配置すれば良いのかが謎です。。。

[winterboum]

質問の最初は ｍｙｓｑｌ２がインストール出来ない、ということでした
次のcapstroのlogでは　Permission denied (publickey).
fatal: Could not read from remote repository.　となっています。
最後は「インストールはされたような記述が書かれているのですが、デプロイ時には
同じエラーが出現しました。」
とあります。

時系列があるので状況がはっきりしません。
現在の状態ではどうなるのでしょう。
何が通り、何が通らないのか。

[Naoto1]

時系列が逆になってしまって申し訳ないです。
現在は、permissionエラーは解決しました。
mysqlのエラーのみ残っている状況です。

分かりづらい説明になってしまいました。

[winterboum]

mysqlのエラー　とは？