[ Started: 2023-03-17 22:50:21 CET ] [ OmnipathR v3.6.2 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ] Hit:1 http://de.archive.ubuntu.com/ubuntu jammy InRelease Get:2 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB] Get:3 http://de.archive.ubuntu.com/ubuntu jammy-updates InRelease [119 kB] Hit:4 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease Get:5 http://de.archive.ubuntu.com/ubuntu jammy-backports InRelease [107 kB] Fetched 336 kB in 0s (696 kB/s) Reading package lists... [1] "Libraries: " "/home/omnipath/local/R/4.3-3.16" [3] "/home/omnipath/local/R/4.3" "/opt/R-devel/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-devel/R-admin.html#Installing-packages 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 36 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 36 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 36 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 36 not to upgrade. 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 36 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 36 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 36 not to upgrade. 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 36 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 36 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 36 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 36 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libgdal-dev is already the newest version (3.4.1+dfsg-1build4). 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 36 not to upgrade. Reading package lists... Building dependency tree... Reading state information... gdal-bin is already the newest version (3.4.1+dfsg-1build4). 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 36 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libgeos-dev is already the newest version (3.10.2-1). 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 36 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libglu1-mesa-dev is already the newest version (9.0.2-1). 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 36 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libgsl-dev is already the newest version (2.7.1+dfsg-3). 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 36 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 packages will be upgraded: jags 1 to upgrade, 0 to newly install, 0 to remove and 35 not to upgrade. Need to get 1,643 kB of archives. After this operation, 123 kB disk space will be freed. Get:1 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ jags 4.3.1-1.2204.1 [1,643 kB] 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 1,643 kB in 0s (5,374 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 ... 635171 files and directories currently installed.) Preparing to unpack .../jags_4.3.1-1.2204.1_amd64.deb ... Unpacking jags (4.3.1-1.2204.1) over (4.3.0-3focal0) ... Setting up jags (4.3.1-1.2204.1) ... 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... libmpfr-dev is already the newest version (4.1.0-3build3). 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 35 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libopenmpi-dev is already the newest version (4.1.2-2ubuntu1). 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 35 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libproj-dev is already the newest version (8.2.1-1). 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 35 not to upgrade. apt-get install -y libcurl4-openssl-dev apt-get install -y libssl-dev 0 0 apt-get install -y libglpk-dev apt-get install -y libgmp3-dev 0 0 apt-get install -y libxml2-dev apt-get install -y make 0 0 apt-get install -y pandoc apt-get install -y libicu-dev 0 0 apt-get install -y libfontconfig1-dev apt-get install -y libfreetype6-dev 0 0 apt-get install -y zlib1g-dev apt-get install -y libgdal-dev 0 0 apt-get install -y gdal-bin apt-get install -y libgeos-dev 0 0 apt-get install -y libglu1-mesa-dev apt-get install -y libgsl0-dev 0 0 apt-get install -y jags apt-get install -y libmpfr-dev 0 0 apt-get install -y libopenmpi-dev apt-get install -y libproj-dev 0 0 [ Finished: 2023-03-17 22:50:38 CET ]