Hello BioDynaMo community!
I cannot seem to beat a problem I have run into with my installation process. I believe I have successfully installed the prerequisites, but the problem occurs when i run the following command:
curl https://biodynamo.org/install | bash
and responds with this error message:
Something went wrong with the installation. For more details check the log file: /tmp/tmp.VeVO3wNXcm/biodynamo/installation.log
For context I am using Ubuntu 20.04.5.
Thanks in advance!
This is the entire response after running the command:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 206 100 206 0 0 509 0 --:–:-- --:–:-- --:–:-- 508
BDM_INSTALL is set to: v1.04-patches
Cloning into ‘.’…
remote: Enumerating objects: 37605, done.
remote: Counting objects: 100% (13148/13148), done.
remote: Compressing objects: 100% (8169/8169), done.
remote: Total 37605 (delta 5485), reused 12233 (delta 4915), pack-reused 24457
Receiving objects: 100% (37605/37605), 97.82 MiB | 14.37 MiB/s, done.
Resolving deltas: 100% (23084/23084), done.
Branch ‘v1.04-patches’ set up to track remote branch ‘v1.04-patches’ from ‘origin’.
Switched to a new branch ‘v1.04-patches’
/tmp/tmp.VeVO3wNXcm/biodynamo
This script installs the following packages with sudo:
clang freeglut3-dev wget
clang-format g++ zlib1g-dev
clang-tidy gcc libbz2-dev
doxygen git libffi-dev
graphviz libblas-dev liblzma-dev
libxml2-dev libbz2-dev libreadline-dev
llvm-7 liblapack-dev libsqlite3-dev
llvm-7-dev libnuma-dev libssl-dev
llvm-7-runtime libomp5 python-openssl
valgrind libomp-dev tk-dev
libgsl-dev libopenmpi-dev xz-utils
cmake libpthread-stubs0-dev zlib1g-dev
curl make
Press any key to continue or Ctrl+C to exit…
Installing prerequisites…
–2023-01-11 09:26:22-- https://apt.llvm.org/llvm-snapshot.gpg.key
Resolving apt.llvm.org (apt.llvm.org)… 151.101.62.49, 2a04:4e42:f::561
Connecting to apt.llvm.org (apt.llvm.org)|151.101.62.49|:443… connected.
HTTP request sent, awaiting response… 200 OK
Length: 3145 (3.1K) [application/octet-stream]
Saving to: ‘llvm-snapshot.gpg.key’
0K ... 100% 1.99M=0.002s
2023-01-11 09:26:22 (1.99 MB/s) - ‘llvm-snapshot.gpg.key’ saved [3145/3145]
[sudo] password for ch00918:
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Hit:1 Index of /ubuntu focal InRelease
Hit:3 Index of /ubuntu focal-updates InRelease
Hit:4 Index of /ubuntu focal-backports InRelease
Hit:5 http://dl.google.com/linux/chrome/deb stable InRelease
Hit:6 Index of /repos/code/ stable InRelease
Get:7 http://apt.insync.io/ubuntu focal InRelease [5,535 B]
Hit:8 Index of /ubuntu/20.04/prod/ focal InRelease
Hit:2 Index of /focal/ llvm-toolchain-focal-10 InRelease
Hit:9 Index of /repos/ms-teams/ stable InRelease
Hit:10 Index of /ubuntu focal-security InRelease
Hit:11 https://apt.kitware.com/ubuntu focal InRelease
Fetched 5,535 B in 1s (7,063 B/s)
Reading package lists…
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Hit:1 Index of /ubuntu focal InRelease
Hit:2 Index of /ubuntu focal-updates InRelease
Hit:3 Index of /ubuntu focal-backports InRelease
Hit:4 Index of /ubuntu focal-security InRelease
Hit:6 http://dl.google.com/linux/chrome/deb stable InRelease
Get:7 http://apt.insync.io/ubuntu focal InRelease [5,535 B]
Hit:8 Index of /repos/code/ stable InRelease
Hit:9 Index of /ubuntu/20.04/prod/ focal InRelease
Hit:10 Index of /repos/ms-teams/ stable InRelease
Hit:5 Index of /focal/ llvm-toolchain-focal-10 InRelease
Hit:11 https://apt.kitware.com/ubuntu focal InRelease
Fetched 5,535 B in 1s (4,878 B/s)
Reading package lists…
Building dependency tree…
Reading state information…
180 packages can be upgraded. Run ‘apt list --upgradable’ to see them.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Hit:1 Index of /ubuntu focal InRelease
Hit:2 Index of /ubuntu focal-security InRelease
Hit:4 Index of /ubuntu focal-updates InRelease
Get:5 http://apt.insync.io/ubuntu focal InRelease [5,535 B]
Hit:6 Index of /ubuntu focal-backports InRelease
Hit:7 http://dl.google.com/linux/chrome/deb stable InRelease
Hit:8 Index of /repos/code/ stable InRelease
Hit:9 Index of /ubuntu/20.04/prod/ focal InRelease
Hit:10 Index of /repos/ms-teams/ stable InRelease
Hit:3 Index of /focal/ llvm-toolchain-focal-10 InRelease
Hit:11 https://apt.kitware.com/ubuntu focal InRelease
Fetched 5,535 B in 6s (976 B/s)
Reading package lists…
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Hit:1 Index of /ubuntu focal InRelease
Hit:2 Index of /ubuntu focal-updates InRelease
Hit:4 Index of /ubuntu focal-backports InRelease
Get:5 http://apt.insync.io/ubuntu focal InRelease [5,535 B]
Hit:6 http://dl.google.com/linux/chrome/deb stable InRelease
Hit:7 Index of /repos/code/ stable InRelease
Hit:8 Index of /ubuntu/20.04/prod/ focal InRelease
Hit:9 Index of /repos/ms-teams/ stable InRelease
Hit:3 Index of /focal/ llvm-toolchain-focal-10 InRelease
Hit:10 Index of /ubuntu focal-security InRelease
Hit:11 https://apt.kitware.com/ubuntu focal InRelease
Fetched 5,535 B in 1s (7,195 B/s)
Reading package lists…
Building dependency tree…
Reading state information…
180 packages can be upgraded. Run ‘apt list --upgradable’ to see them.
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Reading package lists…
Building dependency tree…
Reading state information…
The following packages will be REMOVED
cmake
The following packages will be DOWNGRADED:
cmake-data
0 to upgrade, 0 to newly install, 1 to downgrade, 1 to remove and 180 not to upgrade.
E: Packages were downgraded and -y was used without --allow-downgrades.
Something went wrong with the installation. For more details check the log file: /tmp/tmp.VeVO3wNXcm/biodynamo/installation.log