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ethanbass / chromConverter

Parsers for chromatography data in R (HPLC-DAD/UV, GC-FID, MS)
https://ethanbass.github.io/chromConverter/
GNU General Public License v3.0
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OpenMP error #32

Open dantzler opened 1 month ago

dantzler commented 1 month ago

Using Mac M1. In Rstudio R crashes w/o info. In command line, I get this:

library(chromatographR)
chemstation_file <- "/Users/jeffdantzler/Documents/HPLC/MPA2024-03-1314-04-32.D/"
read_chroms(paths = chemstation_file, format_in = "chemstation_uv")

OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized. OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/ zsh: abort R

ethanbass commented 1 month ago

Hi, Thanks for filing this bug report. Unfortunately, I'm not really sure how to track this one down, since I'm unable to reproduce the error on my machine. I'm thinking this could be due to an issue with the reticulate/python configuration and/or a conflict with data.table which was recently added as a dependency (and makes use of openMP). My best guess is that reticulate may be loading an intel version of OpenMP through rosetta? But I have not seen this error on my M1 mac where I am doing most of the package development.

Some things I can think of to try:

  1. Try the suggested workaround (if you haven't already) by running Sys.setenv(KMP_DUPLICATE_LIB_OK=TRUE) before loading chromConverter.
  2. Revert to an older version of chromConverter prior to the addition of the data.table dependency to test if this is a caused by a conflict with data.table. You should be able to do this by running: remotes::install_github("ethanbass/chromConverter", ref="cfd6d8c1f4caed7b7fb5646c5177fedea2ec8a6c")
  3. Make sure Conda is configured correctly: a. Go to Tools:Global Options in Rstudio and uncheck the box that says Automatically activate project-local Python environments . b. Make sure miniconda is installed by running reticulate::install_miniconda()

Sorry i don't have a better answer. Please do let me know if you figure anything out!

Ethan

dantzler commented 1 month ago

Thank you very much, Ethan. I will try these suggestions and let you know if I figure it out. Have a great weekend! Best regards, Jeff

On Fri, Oct 4, 2024 at 5:02 PM Ethan Bass @.***> wrote:

Hi, Thanks for filing this bug report. Unfortunately, I'm not really sure how to track this one down, since I'm unable to reproduce the error on my machine. I'm thinking this could be due to an issue with the reticulate/python configuration and/or a conflict with data.table which was recently added as a dependency (and makes use of openMP).

Some things I can think of to try:

  1. Try the suggested workaround (if you haven't already) by running Sys.setenv(KMP_DUPLICATE_LIB_OK=TRUE) before loading chromConverter.
  2. Revert to an older version of chromConverter prior to the addition of the data.table dependency to test if this is a caused by a conflict with data.table. You should be able to do this by running: remotes::install_github("ethanbass/chromConverter", ref="cfd6d8c1f4caed7b7fb5646c5177fedea2ec8a6c")
  3. Make sure Conda is configured correctly: a. Go to Tools:Global Options in Rstudio and uncheck the box that says Automatically activate project-local Python environments . b. Make sure miniconda is installed by running reticulate::install_miniconda()

Sorry i don't have a better answer. Please do let me know if you figure anything out!

Ethan

— Reply to this email directly, view it on GitHub https://github.com/ethanbass/chromConverter/issues/32#issuecomment-2394145024, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB3B7WZVBOGVRAUPBKRGNDTZZ3CZ7AVCNFSM6AAAAABPENBHOSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJUGE2DKMBSGQ . You are receiving this because you authored the thread.Message ID: @.***>

ethanbass commented 1 week ago

Hi Jeff, Did you ever manage to figure anything out about this?