[ Started: 2022-12-04 01:12:03 CET ] [ decoupleR v2.3.2 for BioC-3.17 from https://github.com/saezlab/decoupleR@master ] Hit:1 http://de.archive.ubuntu.com/ubuntu focal InRelease Hit:2 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ InRelease Hit:3 http://de.archive.ubuntu.com/ubuntu focal-updates InRelease Hit:4 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal InRelease Hit:5 http://de.archive.ubuntu.com/ubuntu focal-backports InRelease Hit:6 http://security.ubuntu.com/ubuntu focal-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 (66.1-2ubuntu2.1). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libcurl4-openssl-dev is already the newest version (7.68.0-1ubuntu2.14). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libssl-dev is already the newest version (1.1.1f-1ubuntu2.16). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... pandoc is already the newest version (2.5-3build2). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... make is already the newest version (4.2.1-1.2). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libfontconfig1-dev is already the newest version (2.13.1-2ubuntu3). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libfreetype6-dev is already the newest version (2.10.1-2ubuntu0.2). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libfribidi-dev is already the newest version (1.0.8-2ubuntu0.1). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libharfbuzz-dev is already the newest version (2.6.4-1ubuntu4.2). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libjpeg-dev is already the newest version (8c-2ubuntu8). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libpng-dev is already the newest version (1.6.37-2). 0 to upgrade, 0 to newly install, 0 to remove and 56 not to upgrade. Reading package lists... Building dependency tree... Reading state information... 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 53 not to upgrade. Need to get 454 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://de.archive.ubuntu.com/ubuntu focal-updates/main amd64 libtiff-dev amd64 4.1.0+git191117-2ubuntu0.20.04.7 [285 kB] Get:2 http://de.archive.ubuntu.com/ubuntu focal-updates/main amd64 libtiff5 amd64 4.1.0+git191117-2ubuntu0.20.04.7 [163 kB] Get:3 http://de.archive.ubuntu.com/ubuntu focal-updates/main amd64 libtiffxx5 amd64 4.1.0+git191117-2ubuntu0.20.04.7 [5,884 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 454 kB in 0s (3,068 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 ... 557981 files and directories currently installed.) Preparing to unpack .../libtiff-dev_4.1.0+git191117-2ubuntu0.20.04.7_amd64.deb ... Unpacking libtiff-dev:amd64 (4.1.0+git191117-2ubuntu0.20.04.7) over (4.1.0+git191117-2ubuntu0.20.04.6) ... Preparing to unpack .../libtiff5_4.1.0+git191117-2ubuntu0.20.04.7_amd64.deb ... Unpacking libtiff5:amd64 (4.1.0+git191117-2ubuntu0.20.04.7) over (4.1.0+git191117-2ubuntu0.20.04.6) ... Preparing to unpack .../libtiffxx5_4.1.0+git191117-2ubuntu0.20.04.7_amd64.deb ... Unpacking libtiffxx5:amd64 (4.1.0+git191117-2ubuntu0.20.04.7) over (4.1.0+git191117-2ubuntu0.20.04.6) ... Setting up libtiff5:amd64 (4.1.0+git191117-2ubuntu0.20.04.7) ... Setting up libtiffxx5:amd64 (4.1.0+git191117-2ubuntu0.20.04.7) ... Setting up libtiff-dev:amd64 (4.1.0+git191117-2ubuntu0.20.04.7) ... Processing triggers for man-db (2.9.1-1) ... Processing triggers for libc-bin (2.31-0ubuntu9.9) ... Reading package lists... Building dependency tree... Reading state information... libxml2-dev is already the newest version (2.9.10+dfsg-5ubuntu0.20.04.4). 0 to upgrade, 0 to newly install, 0 to remove and 53 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libglpk-dev is already the newest version (4.65-2). 0 to upgrade, 0 to newly install, 0 to remove and 53 not to upgrade. Reading package lists... Building dependency tree... Reading state information... libgmp3-dev is already the newest version (2:6.2.0+dfsg-4ubuntu0.1). 0 to upgrade, 0 to newly install, 0 to remove and 53 not to upgrade. Reading package lists... Building dependency tree... Reading state information... python3 is already the newest version (3.8.2-0ubuntu2). 0 to upgrade, 0 to newly install, 0 to remove and 53 not to upgrade. Reading package lists... Building dependency tree... Reading state information... zlib1g-dev is already the newest version (1:1.2.11.dfsg-2ubuntu1.5). 0 to upgrade, 0 to newly install, 0 to remove and 53 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: 2022-12-04 01:12:26 CET ]