W: Failed to fetch http://llvm.org/apt/precise/dists/llvm-toolchain-precise/main/binary-i386/Packages 404 Not Found W: Failed to fetch http://llvm.org/apt/precise/dists/llvm-toolchain-precise-3.5/main/source/Sources 404 Not Found W: Failed to fetch http://llvm.org/apt/precise/dists/llvm-toolchain-precise-3.5/main/binary-i386/Packages 404 Not Found W: Failed to fetch http://llvm.org/apt/precise/dists/llvm-toolchain-precise-3.6/main/source/Sources 404 Not Found W: Failed to fetch http://llvm.org/apt/precise/dists/llvm-toolchain-precise-3.6/main/binary-i386/Packages 404 Not Found W: Some index files failed to download. They have been ignored, or old ones used instead. E: Could not get lock /var/lib/dpkg/lock - open (11: Resource temporarily unavailable) E: Unable to lock the administration directory (/var/lib/dpkg/), is another process using it? i@scheherezade:/opt/R-3.3.0$ sudo apt-get upgrade --fix-missing Reading package lists... Done Building dependency tree Reading state information... Done The following packages have been kept back: gcc-5-base libatomic1 libgcc1 libgfortran3 libgomp1 libitm1 libobjc4 libquadmath0 libstdc++6 linux-generic-pae linux-headers-generic-pae linux-image-generic-pae linux-tools mopidy python-cffi The following packages will be upgraded: binutils dosfstools firefox firefox-globalmenu firefox-locale-en google-chrome-stable google-cloud-sdk imagemagick imagemagick-common libgd2-xpm libmagick++4 libmagickcore4 libmagickcore4-extra libmagickwand4 libxml2 libxml2-dev libxml2-doc libxml2-utils linux-libc-dev linux-tools-common perlmagick python-libxml2 squid squid3 squid3-common 25 upgraded, 0 newly installed, 0 to remove and 15 not upgraded. Need to get 111 MB/119 MB of archives. After this operation, 4,869 kB of additional disk space will be used. Do you want to continue [Y/n]? Y Err http://dl.google.com/linux/chrome/deb/ stable/main google-chrome-stable i386 48.0.2564.116-1 404 Not Found Get:1 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main firefox i386 47.0+build3-0ubuntu0.12.04.1 [54.0 MB] Get:2 http://packages.cloud.google.com/apt/ cloud-sdk-precise/main google-cloud-sdk all 113.0.0-0 [5,761 kB] Get:3 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main firefox-globalmenu i386 47.0+build3-0ubuntu0.12.04.1 [8,968 B] Get:4 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main firefox-locale-en i386 47.0+build3-0ubuntu0.12.04.1 [761 kB] Get:5 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main linux-libc-dev i386 3.2.0-104.145 [860 kB] Get:6 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main linux-tools-common all 3.2.0-104.145 [66.6 kB] Get:7 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main squid3 i386 3.1.19-1ubuntu3.12.04.7 [1,524 kB] Get:8 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main squid3-common all 3.1.19-1ubuntu3.12.04.7 [122 kB] Get:9 http://us.archive.ubuntu.com/ubuntu/ precise-updates/universe squid i386 3.1.19-1ubuntu3.12.04.7 [6,252 B] Fetched 63.1 MB in 41s (1,526 kB/s) Failed to fetch http://dl.google.com/linux/chrome/deb/pool/main/g/google-chrome-stable/google-chrome-stable_48.0.2564.116-1_i386.deb 404 Not Found (Reading database ... 1096191 files and directories currently installed.) Preparing to replace libxml2-dev 2.7.8.dfsg-5.1ubuntu4.14 (using .../libxml2-dev_2.7.8.dfsg-5.1ubuntu4.15_i386.deb) ... Unpacking replacement libxml2-dev ... Preparing to replace libxml2 2.7.8.dfsg-5.1ubuntu4.14 (using .../libxml2_2.7.8.dfsg-5.1ubuntu4.15_i386.deb) ... Unpacking replacement libxml2 ... Preparing to replace libgd2-xpm 2.0.36~rc1~dfsg-6ubuntu2 (using .../libgd2-xpm_2.0.36~rc1~dfsg-6ubuntu2.1_i386.deb) ... Unpacking replacement libgd2-xpm ... Preparing to replace dosfstools 3.0.12-1ubuntu1.2 (using .../dosfstools_3.0.12-1ubuntu1.3_i386.deb) ... Unpacking replacement dosfstools ... Preparing to replace binutils 2.22-6ubuntu1.3 (using .../binutils_2.22-6ubuntu1.4_i386.deb) ... Unpacking replacement binutils ... Preparing to replace firefox 46.0.1+build1-0ubuntu0.12.04.2 (using .../firefox_47.0+build3-0ubuntu0.12.04.1_i386.deb) ... Unpacking replacement firefox ... Preparing to replace firefox-globalmenu 46.0.1+build1-0ubuntu0.12.04.2 (using .../firefox-globalmenu_47.0+build3-0ubuntu0.12.04.1_i386.deb) ... Unpacking replacement firefox-globalmenu ... Preparing to replace firefox-locale-en 46.0.1+build1-0ubuntu0.12.04.2 (using .../firefox-locale-en_47.0+build3-0ubuntu0.12.04.1_i386.deb) ... Unpacking replacement firefox-locale-en ... Preparing to replace google-cloud-sdk 111.0.0-0 (using .../google-cloud-sdk_113.0.0-0_all.deb) ... Unpacking replacement google-cloud-sdk ... Preparing to replace imagemagick-common 8:6.6.9.7-5ubuntu3.3 (using .../imagemagick-common_8%3a6.6.9.7-5ubuntu3.4_all.deb) ... Unpacking replacement imagemagick-common ... Preparing to replace libmagickcore4 8:6.6.9.7-5ubuntu3.3 (using .../libmagickcore4_8%3a6.6.9.7-5ubuntu3.4_i386.deb) ... Unpacking replacement libmagickcore4 ... Preparing to replace libmagickwand4 8:6.6.9.7-5ubuntu3.3 (using .../libmagickwand4_8%3a6.6.9.7-5ubuntu3.4_i386.deb) ... Unpacking replacement libmagickwand4 ... Preparing to replace imagemagick 8:6.6.9.7-5ubuntu3.3 (using .../imagemagick_8%3a6.6.9.7-5ubuntu3.4_i386.deb) ... Unpacking replacement imagemagick ... Preparing to replace libmagick++4 8:6.6.9.7-5ubuntu3.3 (using .../libmagick++4_8%3a6.6.9.7-5ubuntu3.4_i386.deb) ... Unpacking replacement libmagick++4 ... Preparing to replace libmagickcore4-extra 8:6.6.9.7-5ubuntu3.3 (using .../libmagickcore4-extra_8%3a6.6.9.7-5ubuntu3.4_i386.deb) ... Unpacking replacement libmagickcore4-extra ... Preparing to replace libxml2-doc 2.7.8.dfsg-5.1ubuntu4.14 (using .../libxml2-doc_2.7.8.dfsg-5.1ubuntu4.15_all.deb) ... Unpacking replacement libxml2-doc ... Preparing to replace libxml2-utils 2.7.8.dfsg-5.1ubuntu4.14 (using .../libxml2-utils_2.7.8.dfsg-5.1ubuntu4.15_i386.deb) ... Unpacking replacement libxml2-utils ... Preparing to replace linux-libc-dev 3.2.0-102.142 (using .../linux-libc-dev_3.2.0-104.145_i386.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace linux-tools-common 3.2.0-102.142 (using .../linux-tools-common_3.2.0-104.145_all.deb) ... Unpacking replacement linux-tools-common ... Preparing to replace perlmagick 8:6.6.9.7-5ubuntu3.3 (using .../perlmagick_8%3a6.6.9.7-5ubuntu3.4_i386.deb) ... Unpacking replacement perlmagick ... Preparing to replace python-libxml2 2.7.8.dfsg-5.1ubuntu4.14 (using .../python-libxml2_2.7.8.dfsg-5.1ubuntu4.15_i386.deb) ... Unpacking replacement python-libxml2 ... Preparing to replace squid3 3.1.19-1ubuntu3.12.04.6 (using .../squid3_3.1.19-1ubuntu3.12.04.7_i386.deb) ... squid3 stop/waiting Unpacking replacement squid3 ... Preparing to replace squid3-common 3.1.19-1ubuntu3.12.04.6 (using .../squid3-common_3.1.19-1ubuntu3.12.04.7_all.deb) ... Unpacking replacement squid3-common ... Preparing to replace squid 3.1.19-1ubuntu3.12.04.6 (using .../squid_3.1.19-1ubuntu3.12.04.7_i386.deb) ... Unpacking replacement squid ... Processing triggers for man-db ... Processing triggers for bamfdaemon ... Rebuilding /usr/share/applications/bamf.index... Processing triggers for desktop-file-utils ... Processing triggers for gnome-menus ... Processing triggers for menu ... Processing triggers for doc-base ... Processing 1 changed doc-base file... Registering documents with scrollkeeper... Processing triggers for ureadahead ... Processing triggers for ufw ... Setting up libxml2 (2.7.8.dfsg-5.1ubuntu4.15) ... Setting up libxml2-dev (2.7.8.dfsg-5.1ubuntu4.15) ... Setting up libgd2-xpm (2.0.36~rc1~dfsg-6ubuntu2.1) ... Setting up dosfstools (3.0.12-1ubuntu1.3) ... Setting up binutils (2.22-6ubuntu1.4) ... Setting up firefox (47.0+build3-0ubuntu0.12.04.1) ... Please restart all running instances of firefox, or you will experience problems. Setting up firefox-globalmenu (47.0+build3-0ubuntu0.12.04.1) ... Setting up firefox-locale-en (47.0+build3-0ubuntu0.12.04.1) ... Setting up google-cloud-sdk (113.0.0-0) ... Setting up imagemagick-common (8:6.6.9.7-5ubuntu3.4) ... Installing new version of config file /etc/ImageMagick/delegates.xml ... Installing new version of config file /etc/ImageMagick/policy.xml ... Setting up libmagickcore4 (8:6.6.9.7-5ubuntu3.4) ... Setting up libmagickwand4 (8:6.6.9.7-5ubuntu3.4) ... Setting up imagemagick (8:6.6.9.7-5ubuntu3.4) ... Setting up libmagick++4 (8:6.6.9.7-5ubuntu3.4) ... Setting up libmagickcore4-extra (8:6.6.9.7-5ubuntu3.4) ... Setting up libxml2-doc (2.7.8.dfsg-5.1ubuntu4.15) ... Setting up libxml2-utils (2.7.8.dfsg-5.1ubuntu4.15) ... Setting up linux-libc-dev (3.2.0-104.145) ... Setting up linux-tools-common (3.2.0-104.145) ... Setting up perlmagick (8:6.6.9.7-5ubuntu3.4) ... Setting up python-libxml2 (2.7.8.dfsg-5.1ubuntu4.15) ... Setting up squid3-common (3.1.19-1ubuntu3.12.04.7) ... Setting up squid3 (3.1.19-1ubuntu3.12.04.7) ... Creating Squid HTTP proxy 3.x spool directory structure 2016/06/10 18:21:16| Creating Swap Directories squid3 start/running, process 1110 Setting up squid (3.1.19-1ubuntu3.12.04.7) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place /sbin/ldconfig.real: /usr/local/lib/libstdc++.so.6.0.21-gdb.py is not an ELF file - it has the wrong magic bytes at the start. Processing triggers for menu ... i@scheherezade:/opt/R-3.3.0$