[ Started: 2023-02-14 01:01:53 CET ]
[ cosmosR v1.5.1 for BioC-3.16 from https://github.com/saezlab/cosmosR@master ]

Hit:1 http://security.ubuntu.com/ubuntu jammy-security InRelease
Hit:2 http://de.archive.ubuntu.com/ubuntu jammy InRelease
Hit:3 http://de.archive.ubuntu.com/ubuntu jammy-updates InRelease
Hit:4 http://de.archive.ubuntu.com/ubuntu jammy-backports InRelease
Reading package lists...
[1] "Libraries: "                     "/home/omnipath/local/R/4.2-3.16"
[3] "/home/omnipath/local/R/4.2"      "/usr/lib/R/library"             
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 78 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 78 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 78 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 78 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 78 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 78 not to upgrade.
apt-get install -y libglpk-dev apt-get install -y libgmp3-dev 
                             0                              0 
apt-get install -y libxml2-dev  apt-get install -y libicu-dev 
                             0                              0 
     apt-get install -y pandoc        apt-get install -y make 
                             0                              0 
[ Finished: 2023-02-14 01:01:58 CET ]