DoE Running Begin... Your OS is Windows, there might be unexpected errors. If there is some unexpected bugs, please reduce the 'core' as 1. Error in system("wmic OS get TotalVisibleMemorySize /Value", intern = TRUE) : 'wmic' not found
Traceback to:
system("wmic OS get TotalVisibleMemorySize /Value", intern = TRUE)
9: is.factor(x)
8: gsub("TotalVisibleMemorySize=", "", system("wmic OS get TotalVisibleMemorySize /Value", intern = TRUE)[3])
7: is.factor(x)
6: gsub("\r", "", gsub("TotalVisibleMemorySize=", "", system("wmic OS get TotalVisibleMemorySize /Value", intern = TRUE)[3]))
5: ExperimentsCluster_doe(object = object, object_mslevel = object_mslevel, params = params, isotopeIdentification = isotopeIdentification, BPPARAM = BPPARAM, nSlaves = nSlaves, iterator = iterator)
4: optimizxcms.doe.peakpicking(object = raw_data, params = Parameters, BPPARAM = bp, nSlaves = ncore, subdir = NULL, plot = FALSE)
3: optimize.xcms.doe(raw_data, param = param, ncore = ncore)
2: OptiLCMS::PerformParamsOptimization(mSet = mSet, param = param, method = method, ncore = ncore, running.controller = running.controller)
1: PerformParamsOptimization(mSet, param = SetPeakParam(platform = "HPLC-Q/TOF", polarity = polarity_tag), ncore = 10)
Wmic is no longer supported by new Windows.
To fix this I follow the suggestion from chatgpt
In ExperimentsCluster_doe(), change this Windows block:
memtotal <-
ceiling(as.numeric(gsub(
"\r", "", gsub(
"TotalVisibleMemorySize=",
"",
system('wmic OS get TotalVisibleMemorySize /Value', intern = TRUE)[3]
)
)) / 1024 / 1024)
Replace with
memtotal <- tryCatch(
ceiling(as.numeric(gsub(
"\r", "", gsub(
"TotalVisibleMemorySize=",
"",
system('wmic OS get TotalVisibleMemorySize /Value', intern = TRUE)[3]
)
)) / 1024 / 1024),
error = function(e) NA_real_
)
or you can also manually write your computer memory in like memtotal <-64 *0.6 this "0.6" is giving some buffer, "64" is 64GB.
DoE Running Begin... Your OS is Windows, there might be unexpected errors. If there is some unexpected bugs, please reduce the 'core' as 1. Error in system("wmic OS get TotalVisibleMemorySize /Value", intern = TRUE) : 'wmic' not found
Traceback to:
system("wmic OS get TotalVisibleMemorySize /Value", intern = TRUE)
9: is.factor(x)
8: gsub("TotalVisibleMemorySize=", "", system("wmic OS get TotalVisibleMemorySize /Value", intern = TRUE)[3])
7: is.factor(x)
6: gsub("\r", "", gsub("TotalVisibleMemorySize=", "", system("wmic OS get TotalVisibleMemorySize /Value", intern = TRUE)[3]))
5: ExperimentsCluster_doe(object = object, object_mslevel = object_mslevel, params = params, isotopeIdentification = isotopeIdentification, BPPARAM = BPPARAM, nSlaves = nSlaves, iterator = iterator)
4: optimizxcms.doe.peakpicking(object = raw_data, params = Parameters, BPPARAM = bp, nSlaves = ncore, subdir = NULL, plot = FALSE)
3: optimize.xcms.doe(raw_data, param = param, ncore = ncore)
2: OptiLCMS::PerformParamsOptimization(mSet = mSet, param = param, method = method, ncore = ncore, running.controller = running.controller)
1: PerformParamsOptimization(mSet, param = SetPeakParam(platform = "HPLC-Q/TOF", polarity = polarity_tag), ncore = 10)
Wmic is no longer supported by new Windows.
To fix this I follow the suggestion from chatgpt
In ExperimentsCluster_doe(), change this Windows block:
memtotal <-
ceiling(as.numeric(gsub(
"\r", "", gsub(
"TotalVisibleMemorySize=",
"",
system('wmic OS get TotalVisibleMemorySize /Value', intern = TRUE)[3]
)
)) / 1024 / 1024)
Replace with
memtotal <- tryCatch(
ceiling(as.numeric(gsub(
"\r", "", gsub(
"TotalVisibleMemorySize=",
"",
system('wmic OS get TotalVisibleMemorySize /Value', intern = TRUE)[3]
)
)) / 1024 / 1024),
error = function(e) NA_real_
)
or you can also manually write your computer memory in like memtotal <-64 *0.6 this "0.6" is giving some buffer, "64" is 64GB.