[ Started: 2023-03-07 01:03:31 CET ] [ decoupleR v2.3.3 for BioC-3.17 from https://github.com/saezlab/decoupleR@master ] Hit:1 http://de.archive.ubuntu.com/ubuntu jammy InRelease Hit:2 http://de.archive.ubuntu.com/ubuntu jammy-updates InRelease Hit:3 http://de.archive.ubuntu.com/ubuntu jammy-backports InRelease Hit:4 http://security.ubuntu.com/ubuntu jammy-security InRelease Reading package lists... [1] "Libraries: " "/home/omnipath/local/R/4.2-3.17" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" Warning message: package ‘BiocCheck’ is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages Reading package lists... Building dependency tree... Reading state information... libicu-dev is already the newest version (70.1-2). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libcurl4-openssl-dev is already the newest version (7.81.0-1ubuntu1.8). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libssl-dev is already the newest version (3.0.2-0ubuntu1.8). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... pandoc is already the newest version (2.9.2.1-3ubuntu2). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... make is already the newest version (4.3-4.1build1). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libfontconfig1-dev is already the newest version (2.13.1-4.2ubuntu5). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libfreetype6-dev is already the newest version (2.11.1+dfsg-1ubuntu0.1). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libfribidi-dev is already the newest version (1.0.8-2ubuntu3.1). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libharfbuzz-dev is already the newest version (2.7.4-1ubuntu3.1). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libjpeg-dev is already the newest version (8c-2ubuntu10). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libpng-dev is already the newest version (1.6.37-3build5). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 139 not to upgrade. Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: libtiff5 libtiffxx5 The following packages will be upgraded: libtiff-dev libtiff5 libtiffxx5 3 to upgrade, 0 to newly install, 0 to remove and 136 not to upgrade. Need to get 502 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://de.archive.ubuntu.com/ubuntu jammy-updates/main amd64 libtiff-dev amd64 4.3.0-6ubuntu0.4 [314 kB] Get:2 http://de.archive.ubuntu.com/ubuntu jammy-updates/main amd64 libtiff5 amd64 4.3.0-6ubuntu0.4 [183 kB] Get:3 http://de.archive.ubuntu.com/ubuntu jammy-updates/main amd64 libtiffxx5 amd64 4.3.0-6ubuntu0.4 [5,734 B] debconf: Unable to initialise frontend: Dialog debconf: (Dialogue frontend will not work on a dumb terminal, an Emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: Unable to initialise frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: Unable to re-open stdin: Fetched 502 kB in 0s (3,543 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 635016 files and directories currently installed.) Preparing to unpack .../libtiff-dev_4.3.0-6ubuntu0.4_amd64.deb ... Unpacking libtiff-dev:amd64 (4.3.0-6ubuntu0.4) over (4.3.0-6ubuntu0.3) ... Preparing to unpack .../libtiff5_4.3.0-6ubuntu0.4_amd64.deb ... Unpacking libtiff5:amd64 (4.3.0-6ubuntu0.4) over (4.3.0-6ubuntu0.3) ... Preparing to unpack .../libtiffxx5_4.3.0-6ubuntu0.4_amd64.deb ... Unpacking libtiffxx5:amd64 (4.3.0-6ubuntu0.4) over (4.3.0-6ubuntu0.3) ... Setting up libtiff5:amd64 (4.3.0-6ubuntu0.4) ... Setting up libtiffxx5:amd64 (4.3.0-6ubuntu0.4) ... Setting up libtiff-dev:amd64 (4.3.0-6ubuntu0.4) ... Processing triggers for man-db (2.10.2-1) ... Processing triggers for libc-bin (2.35-0ubuntu3.1) ... Reading package lists... Building dependency tree... Reading state information... libxml2-dev is already the newest version (2.9.13+dfsg-1ubuntu0.2). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 136 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libglpk-dev is already the newest version (5.0-1). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 136 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libgmp3-dev is already the newest version (2:6.2.1+dfsg-3ubuntu1). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 136 not to upgrade. Reading package lists... Building dependency tree... Reading state information... python3 is already the newest version (3.10.6-1~22.04). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 136 not to upgrade. Reading package lists... Building dependency tree... Reading state information... zlib1g-dev is already the newest version (1:1.2.11.dfsg-2ubuntu9.2). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 136 not to upgrade. apt-get install -y libicu-dev apt-get install -y libcurl4-openssl-dev 0 0 apt-get install -y libssl-dev apt-get install -y pandoc 0 0 apt-get install -y make apt-get install -y libfontconfig1-dev 0 0 apt-get install -y libfreetype6-dev apt-get install -y libfribidi-dev 0 0 apt-get install -y libharfbuzz-dev apt-get install -y libjpeg-dev 0 0 apt-get install -y libpng-dev apt-get install -y libtiff-dev 0 0 apt-get install -y libxml2-dev apt-get install -y libglpk-dev 0 0 apt-get install -y libgmp3-dev apt-get install -y python3 0 0 apt-get install -y zlib1g-dev 0 [ Finished: 2023-03-07 01:03:50 CET ]