[ Started: 2023-06-24 18:29:02 CEST ]
[ cosmosR v1.5.2 for BioC-3.17 from https://github.com/saezlab/cosmosR@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...
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...
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...
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.
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.
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: 2023-06-24 18:29:06 CEST ]