snakemake fails with glpk-utils installed
Affects | Status | Importance | Assigned to | Milestone | |
---|---|---|---|---|---|
snakemake (Ubuntu) |
New
|
Undecided
|
Unassigned |
Bug Description
Take the simplest Snakefile possible:
```
rule test:
shell:
'echo Hello'
```
Running snakemake on this file fails with error message:
GLPSOL--GLPK LP/MIP Solver 5.0
Parameter(s) specified in the command line:
--cpxlp /tmp/11746-pulp.lp -o /tmp/11746-pulp.sol
Reading problem data from '/tmp/11746-
/tmp/11746-pulp.lp:5: missing constraint sense
CPLEX LP file processing error
Traceback (most recent call last):
File "/usr/lib/
success = workflow.execute(
File "/usr/lib/
success = scheduler.
File "/usr/lib/
else self.job_
File "/usr/lib/
prob.solve()
File "/usr/lib/
status = solver.
File "/usr/lib/
raise PulpSolverError
pulp.solvers.
A workaround is to uninstall the package glpk-utils.
ProblemType: Bug
DistroRelease: Ubuntu 21.04
Package: snakemake 5.24.1-2
ProcVersionSign
Uname: Linux 5.11.0-17-generic x86_64
NonfreeKernelMo
ApportVersion: 2.20.11-0ubuntu65
Architecture: amd64
CasperMD5CheckR
CurrentDesktop: ubuntu:GNOME
Date: Wed May 19 14:25:48 2021
InstallationDate: Installed on 2021-01-19 (119 days ago)
InstallationMedia: Ubuntu 20.10 "Groovy Gorilla" - Release amd64 (20201022)
PackageArchitec
SourcePackage: snakemake
UpgradeStatus: Upgraded to hirsute on 2021-04-27 (22 days ago)
This may have been fixed: in Debian, snakemake still passes its tests if glpk-utils is installed.