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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