running error in disaggregating MAgPIE land pools

[Jingcheng-Yang]

Dear developers,

My MAgPIE model used to run successfully, but recently an error occurred during the disaggregation of MAgPIE land pools. As a result, some key outputs such as cell.land_0.5_share were not generated. I’ve tried reinstalling MAgPIE, but the issue persists. One of my colleagues also encountered this error but we didn't make any changes for MAgPIE code. Details for this error are described below, and I’ve also attached the full.log file here.
full.log
Could you kindly provide any insights or suggestions on how to resolve this issue? Many thanks in advance for your time and support!

Starting MAgPIE...

MAgPIE run finished!
Model finished with modelstat 2:Local optimal solution achieved.
Cannot access run statistics repository /p/projects/rd3mod/models/statistics/magpie Run statistics are not submitted.

Generating lockfile... done.

output_check.R -> /Users/jc/magpie/output/default_2025-07-30_20.33.32
Output looks good, no problems found!

extra/disaggregation.R -> /Users/jc/magpie/output/default_2025-07-30_20.33.32

Attaching package: ‘dplyr’

The following object is masked from ‘package:magclass’:

where

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Disaggregating conservation land
Write outputs cell.conservation_land
Disaggregating peatland
Disaggregating MAgPIE land pools
Error in withAlignedDims(function(...) base::pmin(..., na.rm = na.rm), :
pmin expects magpie objects with the same items in all dimensions

rds_report.R -> /Users/jc/magpie/output/default_2025-07-30_20.33.32
Start getReport(gdx)...
reportPopulation(gdx) success 0.12s
reportWorkingAgePopulation(gdx) success 0.15s
reportIncome(gdx,type='ppp') success 0.04s
reportIncome(gdx,type='mer') success 0.038s
reportPriceGHG(gdx) success 0.31s
reportFoodExpenditure(gdx) success 10.08s
reportKcal(gdx,detail=detail) success 0.39s
reportProtein(gdx,detail=detail) success 0.25s
reportIntakeDetailed(gdx,detail=detail) success 0.22s
reportAnthropometrics(gdx) success 2.77s
reportLivestockShare(gdx) success 0.15s
reportLivestockDemStructure(gdx) success 0.19s
reportVegfruitShare(gdx) success 0.15s
reportPriceShock(gdx) no return value 0.004s
reportPriceElasticities(gdx) success 1.54s
reportDemand(gdx,detail=detail) success 1.10s
reportDemandBioenergy(gdx,detail=detail) success 0.70s
reportFeed(gdx,detail=detail) success 0.69s
reportProduction(gdx,detail=detail) success 0.11s
reportProductionBioenergy(gdx,detail=detail) success 0.14s
reportTrade(gdx,detail=detail) success 2.06s
reportLandUse(gdx) success 0.75s
reportLandUseChange(gdx) success 0.73s
reportNetForestChange(gdx) success 0.59s
reportPeatland(gdx) success 0.068s
reportLandConservation(gdx) success 0.13s
reportCroparea(gdx,detail=detail) success 0.31s
reportNitrogenBudgetCropland(gdx, dir = dir) success 0.65s
reportNitrogenBudgetPasture(gdx, dir = dir) success 0.10s
reportNitrogenEfficiencies(gdx) success 0.81s
reportManure(gdx) success 0.079s
reportNitrogenPollution(gdx, dir = dir) ERROR 1.92s
reportYields(gdx,detail=detail, physical = TRUE) success 0.77s
reportYields(gdx,detail=detail, physical = FALSE) success 0.77s
reportYieldsCropCalib(gdx,detail=detail) success 0.74s
reportYieldsCropRaw(gdx,detail=detail) success 0.76s
reportFeedConversion(gdx) success 0.32s
reportTau(gdx) success 0.18s
reportTc(gdx) success 0.28s
reportAgriResearchIntensity(gdx) success 0.063s
reportEmissions(gdx) success 178.30s
reportEmissionsBeforeTechnicalMitigation(gdx) success 0.19s
reportCosts(gdx) success 1.50s
reportCostsPresolve(gdx) no return value 0.003s
reportCostTransport(gdx) success 0.15s
reportCostsFertilizer(gdx) success 0.12s
reportCostOverall(gdx) success 0.055s
reportCostCapitalStocks(gdx) success 0.073s
reportCostCapitalInvestment(gdx) success 0.10s
reportCostInputsCrop(gdx) ERROR 0.001s
reportCostsInputFactors(gdx) success 0.27s
reportCostsAccounting(gdx) success 3.03s
reportCostsWithoutIncentives(gdx) success 3.35s
reportAgGDP(gdx) success 0.58s
reportConsumVal(gdx) success 0.25s
reportPriceFoodIndex(gdx,baseyear = 'y2010') success 1.59s
reportPriceFoodIndex(gdx,baseyear = 'y2020') success 1.58s
reportProducerPriceIndex(gdx) success 0.45s
reportExpenditureFoodIndex(gdx) success 38.98s
reportPriceAgriculture(gdx) success 0.068s
reportPriceBioenergy(gdx) success 0.068s
reportPriceLand(gdx) success 0.096s
reportPriceWater(gdx) success 0.081s
reportValueTrade(gdx) success 1.45s
reportProcessing(gdx, indicator='primary_to_process') success 0.11s
reportProcessing(gdx, indicator='secondary_from_primary') success 0.27s
reportAEI(gdx) success 0.048s
reportWaterUsage(gdx, detail = FALSE) success 1.59s
reportWaterAvailability(gdx) success 0.025s
reportAAI(gdx) success 0.077s
reportSOM(gdx) success 0.54s
reportGrowingStock(gdx, indicator='relative') success 1.54s
reportGrowingStock(gdx, indicator='absolute') success 1.23s
reportSDG1(gdx) success 0.021s
reportSDG2(gdx) success 8.11s
reportSDG3(gdx) success 2.03s
reportSDG6(gdx) success 0.88s
reportSDG12(gdx) success 1.46s
reportSDG15(gdx) success 1.43s
reportPBwater(gdx, level='regglo') success 1.59s
reportPBland(gdx, dir = dir, level='regglo') ERROR 0.00s
reportPBbiosphere(gdx, dir = dir, level='regglo') ERROR 0.002s
reportPBnitrogen(gdx, dir = dir, level='regglo') ERROR 1.94s
reportForestYield(gdx) success 0.77s
reportharvested_area_timber(gdx) success 0.72s
reportPlantationEstablishment(gdx) success 0.20s
reportRotationLength(gdx) success 0.056s
reportTimber(gdx) success 0.24s
reportBII(gdx, dir = dir) ERROR 0.19s
reportCropDiversity(gdx) success 0.38s
reportPriceWoodyBiomass(gdx) success 0.22s
reportCarbonstock(gdx) success 0.13s
reportGrasslandManagement(gdx) Disabled (no managed pastures) 0.022s
reportGrassStats(gdx) Disabled (no managed pastures) 0.003s
reportGrasslandYields(gdx) Disabled (No separate grassland yields) 0.023s
reportLSUGrasslands(gdx) Disabled (No LSU management) 0.008s
reportAgEmployment(gdx, type = 'absolute', detail = TRUE) success 0.13s
reportAgEmployment(gdx, type = 'share', detail = TRUE) success 0.28s
reportHourlyLaborCosts(gdx) success 0.23s
reportRelativeHourlyLaborCosts(gdx) success 0.10s
reportTotalHoursWorked(gdx) success 0.16s
reportOutputPerWorker(gdx) success 0.29s
reportValueMaterialDemand(gdx) success 0.18s
reportFactorCostShares(gdx, type = 'requirements') success 0.33s
reportFactorCostShares(gdx, type = 'optimization') success 0.25s
reportFactorCostShares(gdx, type = 'accounting') success 0.38s
reportWageDevelopment(gdx, baseYear = 2000) success 0.31s
reportWageDevelopment(gdx, baseYear = 2010) success 0.31s
reportWageDevelopment(gdx, baseYear = 2020) success 0.31s
reportWaterIndicators(gdx) success 1.79s
reportBioplasticDemand(gdx) success 0.092s
reportCostsMACCS(gdx) success 0.048s
reportLaborCostsEmpl(gdx) success 0.19s
reportLaborProductivity(gdx) no return value 0.005s
reportRuralDemandShares(gdx, type = 'tradOnly') no return value 0.005s
reportCostsWholesale(gdx) no return value 0.004s
reportFit(gdx,type='R2',level='grid') ERROR 0.065s
reportFit(gdx,type='R2',level='cell') success 10.75s
reportExtraResidueEmissions(gdx, level='regglo') success 0.044s
reportFireEmissions(gdx, level='regglo') success 0.42s
Total runtime: 334.04s

Warning messages:
1: In runsubmit(output = output, alloutputdirs = outputdir, submit = submit, :
Script extra/disaggregation.R was stopped by an error and not executed properly!
2: In eval(exprs[i], envir) :
The following 6 variables are expected in the piamInterfaces package for mapping SHAPE, but cannot be found in the MAgPIE report.
Please either fix in magpie4 or adjust the mapping in piamInterfaces.

• Biodiversity|BII in areas outside Biodiversity Hotspots, Intact Forest & Cropland Landscapes (unitless),
• Biodiversity|Biodiversity Hotspot and Intact Forest Landscapes BII (unitless),
• Biodiversity|Biodiversity Hotspot BII (unitless),
• Biodiversity|Cropland Landscapes BII (unitless),
• Resources|Nitrogen|Pollution|Surplus|Cropland (Mt Nr/yr),
• Resources|Nitrogen|Pollution|Surplus|Non-agricultural land (Mt Nr/yr)

3: In eval(exprs[i], envir) :
The following 1 variables are expected in the piamInterfaces package for mapping AR6_MAgPIE, but cannot be found in the MAgPIE report.
Please either fix in magpie4 or adjust the mapping in piamInterfaces.

• Biodiversity|BII (unitless)

Saving timeGAMSStart, timeGAMSEnd, timeOutputStart and timeOutputStart to runstatistics.rda
Warning messages:
1: In runsubmit(output = output, alloutputdirs = outputdir, ... :
Script extra/disaggregation.R was stopped by an error and not executed properly!
2: In eval(exprs[i], envir) :
The following 6 variables are expected in the piamInterfaces package for mapping SHAPE, but cannot be found in the MAgPIE report.
Please either fix in magpie4 or adjust the mapping in piamInterfaces.

• Biodiversity|BII in areas outside Biodiversity Hotspots, Intact Forest & Cropland Landscapes (unitless),
• Biodiversity|Biodiversity Hotspot and Intact Forest Landscapes BII (unitless),
• Biodiversity|Biodiversity Hotspot BII (unitless),
• Biodiversity|Cropland Landscapes BII (unitless),
• Resources|Nitrogen|Pollution|Surplus|Cropland (Mt Nr/yr),
• Resources|Nitrogen|Pollution|Surplus|Non-agricultural land (Mt Nr/yr)

3: In eval(exprs[i], envir) :
The following 1 variables are expected in the piamInterfaces package for mapping AR6_MAgPIE, but cannot be found in the MAgPIE report.
Please either fix in magpie4 or adjust the mapping in piamInterfaces.

• Biodiversity|BII (unitless)

2025-07-30 21:06:50: unlocked model.

[codeZeilen]

Hi @Jingcheng-Yang ,
sorry for the late reply, I did not see your post at first. The error you saw was the result of a temporarily faulty version of a dependency of magpie. Starting another magpie run and choosing "yes" when it asks you whether to update packages should resolve the issue. Alternatively, you could also run the following in the magpie folder:
Rscript -e "renv::update('magclass')"

If the issue does not resolve: Let me know 🙂