[ Started: 2023-07-04 18:36:30 CEST ] [ progeny v1.17.3 for BioC-3.17 from https://github.com/saezlab/progeny@master ] Reading package lists... E: Could not get lock /var/lib/apt/lists/lock. It is held by process 1234569 (apt-get) E: Unable to lock directory /var/lib/apt/lists/ [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/opt/R-devel/lib/R/library" 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 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libcurl4-openssl-dev is already the newest version (7.81.0-1ubuntu1.10). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libssl-dev is already the newest version (3.0.2-0ubuntu1.10). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 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 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 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 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libxml2-dev is already the newest version (2.9.13+dfsg-1ubuntu0.3). The following packages were automatically installed and are no longer required: gcc-10-base libclang-10-dev libclang-common-10-dev libclang1-10 libllvm10 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 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 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 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 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 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 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 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 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 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 libllvm13 libobjc-9-dev libstdc++-9-dev Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 90 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 libglpk-dev 0 0 apt-get install -y libgmp3-dev apt-get install -y libxml2-dev 0 0 apt-get install -y libpng-dev apt-get install -y python3 0 0 apt-get install -y make apt-get install -y zlib1g-dev 0 0 apt-get install -y pandoc 0 [ Finished: 2023-07-04 18:36:37 CEST ]