Hi,
I installed the DeconBenchmark tool as well as singularity. Everything works fine until I do this:
_methodsToRun <- c("MuSic", "DWLS", "EPIC", "MIXTURE", "digitalDLSorter")
requiredInputs <- getMethodsInputs(methodsToRun, containerEngine = "singularity")
print(requiredInputs)_
And I start getting this message:
_Running singularity run --env PARAMS_OUTPUT_PATH=/tmp/RtmpaBXCE0/bKiedrUnWD/params.csv docker://deconvolution/music:latest
INFO: Using cached SIF image
INFO: Converting SIF file to temporary sandbox...
WARNING: ignoring environment value of R_HOME
During startup -
Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called 'rhdf5'
Calls: loadNamespace ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted_
I am trying to run the tool on an HPC cluster. I have tried to remove every package and re-download it and it still gives the same error.
Any help is appreciated!
Thank you in advance,
Ana
Hi,
I installed the DeconBenchmark tool as well as singularity. Everything works fine until I do this:
_methodsToRun <- c("MuSic", "DWLS", "EPIC", "MIXTURE", "digitalDLSorter")
requiredInputs <- getMethodsInputs(methodsToRun, containerEngine = "singularity")
print(requiredInputs)_
And I start getting this message:
_Running singularity run --env PARAMS_OUTPUT_PATH=/tmp/RtmpaBXCE0/bKiedrUnWD/params.csv docker://deconvolution/music:latest
INFO: Using cached SIF image
INFO: Converting SIF file to temporary sandbox...
WARNING: ignoring environment value of R_HOME
During startup -
Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called 'rhdf5'
Calls: loadNamespace ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted_
I am trying to run the tool on an HPC cluster. I have tried to remove every package and re-download it and it still gives the same error.
Any help is appreciated!
Thank you in advance,
Ana