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Windowsから フォルダがエラーでアクセスできなってしまったので
chkconfig をインストールして Samba サーバーを停止した

raspberrypi ~ $ sudo apt-get install chkconfig
raspberrypi ~ $ sudo chkconfig samba off
raspberrypi ~ $ sudo chkconfig -l

raspberrypi ~ $ sudo apt-get update
raspberrypi ~ $ sudo apt-get upgrade

raspberrypi ~ $ sudo apt-get update
raspberrypi ~ $ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages have been kept back:
fake-hwclock gnome-accessibility-themes gnome-themes-standard
gnome-themes-standard-data libfm-data libfreetype6 libfreetype6-dev
libgail-3-0 libgcc1 libgfortran3 libgomp1 libgtk-3-0 libgtk-3-bin
libgtk-3-common libjavascriptcoregtk-3.0-0 libpango1.0-0 libstdc++6
libwebkitgtk-3.0-0 lxinput lxpanel omxplayer pcmanfm pypy-upstream zenity
zenity-common
The following packages will be upgraded:
apache2 apache2-mpm-worker apache2-utils apache2.2-bin apache2.2-common
bind9 bind9-host bind9utils cups-bsd cups-client cups-common dnsutils
firmware-realtek ghostscript libbind9-80 libcups2 libcupsimage2 libdns88
libexpat1 libgs9 libgs9-common libicu48 libisc84 libisccc80 libisccfg82
liblwres80 libmysqlclient18 libraspberrypi-bin libraspberrypi-dev
libraspberrypi-doc libraspberrypi0 libsdl1.2debian libsqlite3-0 libssl1.0.0
mysql-common openssl raspberrypi-bootloader raspi-config
38 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Need to get 79.5 MB of archives.
After this operation, 2,039 kB of additional disk space will be used.
Do you want to continue [Y/n]? y

~ $ sudo apt-get update
~ $ sudo apt-get upgrade
The following packages have been kept back:
fake-hwclock gnome-accessibility-themes gnome-themes-standard gnome-themes-standard-data libfm-data libfreetype6
libfreetype6-dev libgail-3-0 libgcc1 libgfortran3 libgomp1 libgtk-3-0 libgtk-3-bin libgtk-3-common
libjavascriptcoregtk-3.0-0 libpango1.0-0 libstdc++6 libwebkitgtk-3.0-0 lxinput lxpanel omxplayer pcmanfm
pypy-upstream zenity zenity-common
The following packages will be upgraded:
fuse libfuse2 libpq5 libraspberrypi-bin libraspberrypi-dev libraspberrypi-doc libraspberrypi0
libwebkitgtk-3.0-common ntfs-3g raspberrypi-bootloader raspi-config
11 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Need to get 64.2 MB of archives.
After this operation, 6,113 kB of additional disk space will be used.
Do you want to continue [Y/n]? Y

インストールされているパッケージの一覧を表示するには "dpkg -l" を使う

参考
Debianでのパッケージ管理コマンド一覧

$ sudo apt-get update
$ sudo apt-get upgrade
The following packages have been kept back:
fake-hwclock gnome-accessibility-themes gnome-themes-standard
gnome-themes-standard-data libfm-data libfreetype6 libfreetype6-dev
libgail-3-0 libgcc1 libgfortran3 libgomp1 libgtk-3-0 libgtk-3-bin
libgtk-3-common libjavascriptcoregtk-3.0-0 libpango1.0-0 libstdc++6
libwebkitgtk-3.0-0 lxpanel omxplayer pcmanfm pypy-upstream zenity
zenity-common
The following packages will be upgraded:
bind9 bind9-host bind9utils cups-bsd cups-client cups-common curl dnsutils
dpkg dpkg-dev e2fslibs e2fsprogs file gnupg gpgv libarchive12 libbind9-80
libc-bin libc-dev-bin libc6 libc6-dev libcomerr2 libcups2 libcupsimage2
libcurl3 libcurl3-gnutls libdns88 libdpkg-perl libgcrypt11 libgd2-xpm
libgnutls26 libicu48 libisc84 libisccc80 libisccfg82 libldap-2.4-2
liblwres80 libmagic1 libmysqlclient18 libraspberrypi-bin libraspberrypi-dev
libraspberrypi-doc libraspberrypi0 libsmbclient libss2 libssh2-1 libssl1.0.0
libtasn1-3 libwbclient0 libwebkitgtk-3.0-common libx11-6 libx11-data
libx11-xcb1 libxfont1 libxml2 libxrender1 locales multiarch-support
mysql-common ntp ntpdate openssl raspberrypi-bootloader samba samba-common
smbclient sudo wpagui wpasupplicant xdg-utils
70 upgraded, 0 newly installed, 0 to remove and 24 not upgraded.
Need to get 111 MB of archives.
After this operation, 771 kB disk space will be freed.

/etc/iptables/rules.v4 に pop3 と pop3s を許可するように設定した
実行したコマンド
$ sudo /sbin/iptables-restore --verbose < /etc/iptables/rules.v4

参考にしたページ
Raspberry Pi と iptables - Raspberry Pi を何年か使い続けるブログ

$ sudo apt-get update
$ sudo apt-get upgrade
The following packages have been kept back:
fake-hwclock gnome-accessibility-themes gnome-themes-standard
gnome-themes-standard-data libfm-data libfreetype6
libfreetype6-dev libgail-3-0 libgcc1 libgfortran3 libgomp1 libgtk-3-0 libgtk-3-bin
libgtk-3-common
libjavascriptcoregtk-3.0-0 libpango1.0-0 libstdc++6 libwebkitgtk-3.0-0
lxpanel omxplayer pcmanfm pypy-upstream
zenity zenity-common

The following packages will be upgraded:
apache2 apache2-mpm-worker apache2-utils apache2.2-bin
apache2.2-common base-files bind9 bind9-host bind9utils
bsd-mailx cpio curl dbus dbus-x11 dnsutils dosfstools file
krb5-locales libbind9-80 libc-bin libc-dev-bin libc6
libc6-dev libcurl3 libcurl3-gnutls libdbus-1-3 libdns88 libevent-2.0-5 libflac8
libgssapi-krb5-2 libisc84 libisccc80
libisccfg82 libjasper1 libk5crypto3 libkrb5-3 libkrb5support0 liblwres80
libmagic1 libmysqlclient18 libpixman-1-0
libpq5 libraspberrypi-bin libraspberrypi-dev libraspberrypi-doc libraspberrypi0
libssl1.0.0 libwebkitgtk-3.0-common
libxml2 locales mime-support multiarch-support mysql-common ntp ntpdate
openssl perl perl-base perl-modules
python-rpi.gpio python3-rpi.gpio raspberrypi-artwork raspberrypi-bootloader
raspi-config tzdata unzip xdg-utils
xserver-common xserver-xorg-core
69 upgraded, 0 newly installed, 0 to remove and 24 not upgraded.

通常のパッケージでは，ルートディレクトリを書き込み不可にしないと出来ないのであきらめた

$ sudo apt-get update
$ sudo apt-get upgrade

The following packages have been kept back:
gnome-accessibility-themes
gnome-themes-standard
gnome-themes-standard-data
libgail-3-0 libgcc1
libgfortran3
libgomp1
libgtk-3-0
libgtk-3-bin
libgtk-3-common
libjavascriptcoregtk-3.0-0
libpango1.0-0 libstdc++6
libwebkitgtk-3.0-0
pypy-upstream zenity zenity-common

The following packages will be upgraded:
bind9
bind9-host
bind9utils
binutils
curl
dbus
dbus-x11
dnsutils
file
firmware-brcm80211
glib-networking
glib-networking-common
glib-networking-services
gnupg gpgv
libatk1.0-0
libatk1.0-data
libbind9-80
libcairo-gobject2
libcairo2
libcurl3
libcurl3-gnutls
libdbus-1-3
libdns88
libgdk-pixbuf2.0-0
libgdk-pixbuf2.0-common
libglib2.0-0
libglib2.0-data
libisc84
libisccc80
libisccfg82
liblwres80
libmagic1
liborc-0.4-0
libpcre3
libpixman-1-0
libraspberrypi-bin
libraspberrypi-dev
libraspberrypi-doc
libraspberrypi0
libsoup-gnome2.4-1
libsoup2.4-1
libwebkitgtk-3.0-common
lua5.1 make python-rpi.gpio
python3-rpi.gpio raspberrypi-bootloader
raspi-config

49 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.

Linuxコマンド集 - 【 apt-get 】 パッケージを取得してインストール/アップデートする：ITpro