Issue with PerformParamsOptimization function in metaboanalystR

MetaboAnalyst
1

Hello All! I am using metaboanalystR in macOS Monterey version 12.5.1 (M1,2020 Apple M1, Memory = 16 GB).
I am using metaboanalyst R documentation to do the analysis and I get the following error:

param_optimized ← PerformParamsOptimization(raw_data, param = param_initial, ncore = 6)

Step 1/6: Start to optimize parameters!

This step may take a long time…
DoE Optimization Starting Now… (2023-06-11 18:22:26.219558)
Evaluating Noise level…
ppm is estimated as : 14.1
Done!
Preparing Parameters for optimization finished !
Data Spliting Finished !
Peak Preparing Begin…
Peak Preparing Done !
Round:1
DoE Running Begin…
awk: can’t open file /proc/meminfo
source line number 1
Error in if (memtotal/data.size > 30) { : argument is of length zero
In addition: Warning message:
In system(“awk ‘/MemTotal/ {print $2}’ /proc/meminfo”, intern = TRUE) :
running command ‘awk ‘/MemTotal/ {print $2}’ /proc/meminfo’ had status 2

I am not able to understand what exactly this means.

I used the very first data file (C/091622_RPLC_POS_26C_0003) from the following website:

Metabolomics Workbench : NIH Data Repository?

2

Actually , I managed to solve this problem. Sorry for bringing it up.

Thank you!

3

Hi PB,

I’m having the same problem. May I know how you solve it?

Tqvm

4

Hi Brenda,

I managed to get away with this issue by reducing the ncore to 1. I am not sure if it affects the result in anyway, but I think this leads to slower execution of the optimization process.

Thank you!

1 Like
5

The issue is related to the CPU type. The core code was written in C/C++11 and tested on Linux or Mac OS X equipped with Intel and AMD CPU types. It may not work well on ARM -based CPU (used in Apple M1 chip and Tau VM ).

6

Same issue here, any updates?