Problem with writing permissions on CentOS

[palfalvi]

Hi,

Thank you for your effort, it is a great initiative. I would love to try how babette can fit in some automated pipeline.

I was just trying out babette with some example data, but I got the following issue:

library(babette)

fasta_name <- "anthus_aco.fasta"

mrca_priors <- create_mrca_prior(
  taxa_names = get_taxa_names(fasta_name),
  alignment_id = get_alignment_id(fasta_name),
  mrca_distr = create_normal_distr(mean = 15.0, sigma = 0.025)
)
 
mcmc = create_mcmc(chain_length=2000, store_every = 1000)

out <- bbt_run(fasta_name, mcmc = mcmc, mrca_priors = mrca_priors)

Error: file.exists(output_log_filename) is not TRUE
In addition: Warning messages:
1: In file.rename(from = from, to = output_log_filename) :
  cannot rename file 'anthus_aco.log' to '/tmp/RtmpI5Egd6/beast2_258b458753999log', reason 'Invalid cross-device link'
2: In file.rename(from = from, to = to) :
  cannot rename file 'anthus_aco.trees' to '/tmp/RtmpI5Egd6/beast2_anthus_aco_258b42309a56a.trees', reason 'Invalid cross-device link'

I could not find any workaround for this issue. Do you have any idea how to solve?

Thank you in advance!

Best,
Gergo

[richelbilderbeek]

Hi Gergo, thanks for helping improve babette! I usually get that error when using an encrypted home folder. Do you happen to use such an encrypted home folder?

[palfalvi]

Hi,

Thanks for helping. I am using CentOS7, no encryption and here is the session info:

Session info ------------------------------------------------------------------
 setting  value                       
 version  R version 3.5.0 (2018-04-23)
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       Asia/Tokyo                  
 date     2018-11-12  

[richelbilderbeek]

Hi @palfalvi,

No idea why CentOS7 (with an unencrypted home) fails.

I do know that I use tempfile to create temporary files,
which I feel is the cause,
that apparently somehow fails on CentOS,
like it does on an encrypted home.

As a work-around -it will be ugly, one could specify all temporary files.

These are the defaults:

bbt_run <- function(
  # Your arguments
  beast2_output_log_filename = tempfile(pattern = "beast2_", fileext = "log"),
  beast2_output_trees_filenames = tempfile(
    pattern = paste0(
      "beast2_",
      beautier::get_alignment_ids(fasta_filenames), "_"
    ),
    fileext = ".trees"
  ),
  beast2_output_state_filename = tempfile(
    pattern = "beast2_", fileext = ".xml.state"
  ),
)

Change it to:

bbt_run <- function(
  # Your arguments
  beast2_output_log_filename = "~/beast2.log",
  beast2_output_trees_filenames = paste0("~/", get_alignment_id(fasta_filenames), ".trees"),
  beast2_output_state_filename = "~/beast2.xml.state"
)

I hope that helps. If yes or no, please let me know.

It would help me, to reproduce the bug in a Continuous Integration service.
I use Travis CI for Mac+Ubuntu and AppVeyor for Windows.
If you could set up a third service (Semaphore, Jenkins, anything that is free), I could take a closer look at it.

Cheers, Richel

[richelbilderbeek]

Hi @palfalvi, I've added #33 ('Detect if babette is run on CentOS') to at least give a warning when babette is run on an untested OS.

I am sorry I cannot help as long as I cannot let Travis or AppVeyor produce a CentOS environment. Well, you'll probably notice more often that the *buntus have all the support...

If you find a way for me to help (in a scalable way), I'd be happy to do so 👍

[richelbilderbeek]

This is the reprex, so I can check if it works:

library(babette)

fasta_name <- get_babette_path("anthus_aco.fas")

mrca_priors <- create_mrca_prior(
  taxa_names = get_taxa_names(fasta_name),
  alignment_id = get_alignment_id(fasta_name),
  mrca_distr = create_normal_distr(mean = 15.0, sigma = 0.025)
)

mcmc <- create_mcmc(chain_length = 2000, store_every = 1000)

out <- bbt_run(fasta_name, mcmc = mcmc, mrca_priors = mrca_priors)

Yes, this works on my OS (Lubuntu 16.10) and Travis and AppVeyor.

[richelbilderbeek]

Unhappily closing the Issue 🙁