Closed LojzaZ closed 4 months ago
Hi @LojzaZ - that you for report this issue. The estep
function comes from the mclust
package, that is already installed (it's listed in your session information). I can reproduce the error by running the phenoDisco
example. I will investigate.
Also tagging @lmsimp.
I found the issue and will fix the bug. In the meantime, simply loading and attaching mclust
will fix the error:
library(pRoloc)
library(mclust)
## your code
phenoDisco(...)
Great, thank you very much! Unfortunatelly, even if I attach the mclust package I still get the error. Let's see if its gonna work when you fix the bug.
Oh, that's annoying, as my fix would be the programmatic equivalent of loading mclust
. If you haven't done so, could you restart R, load the packages, and try again, please.
Yes I did and still the same error, I can try installing all the packages on metacentrum since I am planning to run it there anyway (now I am just trying if it runs on my laptop), and see if I get the error.
Not sure what metacentrum is.
If you want to re-install packages, you can install the (hopefully) fixed version with
BiocManager::install("lgatto/pRoloc")
It's weird, as phenoDisco() runs on my computer after restarting, loading pRoloc
and mclust
, and running the example code in ?phenoDisco
. Could you try that.
Here's the exact code (minus the package startup messages) that worked, with the original pRoloc version
> library(pRoloc)
> library(pRolocdata)
> data(tan2009r1)
> pdres <- phenoDisco(tan2009r1, fcol = "PLSDA")
Iteration 1
Stop worker failed with the error: reached CPU time limit
Error: BiocParallel errors
2 remote errors, element index: 1, 11
98 unevaluated and other errors
first remote error:
Error in estep(data = structure(c(1.9527019824844, 2.02054612420664, 1.79267821932411, : could not find function "estep"
> library(mclust)
__ __
____ ___ _____/ /_ _______/ /_
/ __ `__ \/ ___/ / / / / ___/ __/
/ / / / / / /__/ / /_/ (__ ) /_
/_/ /_/ /_/\___/_/\__,_/____/\__/ version 6.1.1
Type 'citation("mclust")' for citing this R package in publications.
> pdres <- phenoDisco(tan2009r1, fcol = "PLSDA")
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
I have confirmed that with the latest version of the package, available with BiocManager::install("lgatto/pRoloc")
(there have been a couple of udpates, the latest being around noon), the code in ?phenoDisco
works.
Thanks again for reporting the problem.I'm closing the issue now, but feel free to re-open it if you still run into the same problem with estep
, estepEEE
, ... not being available.
Thanks, I'll try to reinstall and will see.
Hi, I am trying to run the phenoDisco but I get the following error:
Error
I understand that I am missing the function estep. But I do not know what package it should come from, plus from the example site (https://lgatto.github.io/pRoloc/articles/v01-pRoloc-tutorial.html), I assume that only pRoloc and MSnbase are needed to run this and these I have so I am confused. I am also loading the package stats because if I do not there is also a warning that stats may not be available.
The simplified code:
Session info: