Apptainer image fails with SystemError: mktemp: read-only file system
Running make data/interim
from the Alzheimer repo triggers the following error:
ERROR: LoadError: SystemError: mktemp: Read-only file system
Stacktrace:
[1] systemerror(p::Symbol, errno::Int32; extrainfo::Nothing)
@ Base ./error.jl:176
[2] #systemerror#82
@ ./error.jl:175 [inlined]
[3] systemerror
@ ./error.jl:175 [inlined]
[4] mktemp(parent::String; cleanup::Bool)
@ Base.Filesystem ./file.jl:619
[5] mktemp
@ ./file.jl:616 [inlined]
[6] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
@ Base ./loading.jl:2186
[7] compilecache
@ ./loading.jl:2167 [inlined]
[8] _require(pkg::Base.PkgId, env::String)
@ Base ./loading.jl:1805
[9] _require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1660
[10] macro expansion
@ ./loading.jl:1648 [inlined]
[11] macro expansion
@ ./lock.jl:267 [inlined]
[12] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1611
[13] include(fname::String)
@ Base.MainInclude ./client.jl:478
[14] top-level scope
@ /app/scripts/larvatagger-toolkit.jl:21
in expression starting at /app/src/cli_toolkit.jl:1
in expression starting at /app/scripts/larvatagger-toolkit.jl:21
if variable LARVATAGGER_VERSION is set to 0.17, while no issues are met with version 0.16.4.
EDIT: Version 0.16.4 (and probably all the older versions) is now affected by a very similar issue:
ERROR: LoadError: IOError: open("/usr/local/share/julia/logs/manifest_usage.toml.pid", 194, 292): read-only file system (EROFS)
This issue is likely linked to the Apptainer version as well. It can be fixed as explained below.