Hi Yayan,
Sounds like your names (or loci) have duplicated names and that throws of the function.
Can you try:
indNames(gl) <- make.unique(indNames(gl)) #add .1 etc to duplicates
and potentially also
locNames(gl) <- make.unique(locNames(gl))
That might work.
Cheers, Bernd
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Dear Bernd,
Yes, that's me.
Thanks for the solution to try but unfortunatelly I still get the same error. The results were found as files in the temp folder but unsaved in the R studio as before. The full code and error results are as follows:
# SNP data (use two populations and only the first 100 SNPs)
pops <- possums.gl[1:60, 1:100]
indNames(pops) <- make.unique(indNames(pops)) #add .1 etc to duplicates
#and potentially also
locNames(pops) <- make.unique(locNames(pops))
nes <- gl.LDNe(pops, outfile = "popsLD.txt", neest.path = "./Ne/",
critical = c(0, 0.05), singleton.rm = TRUE, mating = "random")
> nes <- gl.LDNe(pops, outfile = "popsLD.txt", neest.path = "./Ne/",
+ critical = c(0, 0.05), singleton.rm = TRUE, mating = "random")
Starting gl.LDNe
Processing genlight object with SNP data
Starting gl2genepop
Processing genlight object with SNP data
The genepop file is saved as: C:\Users\YAYANK~1\AppData\Local\Temp\RtmpQNzEH6/dummy.gen/
Completed: gl2genepop
Number of loci = 100, 2-digit alleles
Input file: dummy.gen - GENEPOP format
Number of loci = 100, 2-digit alleles
Method(s): LD
Locus names - last 6 characters:
X1 X2 X3 X4 X5 X6 X7 X8 X9 X10
X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
X21 X22 X23 X24 X25 X26 X27 X28 X29 X30
X31 X32 X33 X34 X35 X36 X37 X38 X39 X40
X41 X42 X43 X44 X45 X46 X47 X48 X49 X50
X51 X52 X53 X54 X55 X56 X57 X58 X59 X60
X61 X62 X63 X64 X65 X66 X67 X68 X69 X70
X71 X72 X73 X74 X75 X76 X77 X78 X79 X80
X81 X82 X83 X84 X85 X86 X87 X88 X89 X90
X91 X92 X93 X94 X95 X96 X97 X98 X99 X100
Outputs are written to file popsLD.txt
Tabular-format LD Output File Name: popsLDxLD.txt
Starting time: Thu Oct 23 10:44:53 2025
Population 1 [A_1]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 14.3
Parameter CI: 12.1 16.9
Jackknife CI: 8.6 24.7
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
* For lowest freq: 0.000
Estimate of Ne: 15.1
Parameter CI: 12.9 17.7
Jackknife CI: 9.8 24.1
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
Population 2 [B_31]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
* For lowest freq: 0.000
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
Error in `levels<-`(`*tmp*`, value = as.character(levels)) :
factor level [2] is duplicated
It sounds a simple error but I couldn't figure it out why and how to solve it.
Best,YK
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Workspace loaded from D:/my.R.project/Cinereus/.RData] Loading required package: adegenet Loading required package: ade4 Loading required package: adegenet Loading required package: ade4 /// adegenet 2.1.11 is loaded //////////// > overview: '?adegenet' > tutorials/doc/questions: 'adegenetWeb()' > bug reports/feature requests: adegenetIssues() Loading required package: vcfR ***** *** vcfR *** ***** This is vcfR 1.15.0 browseVignettes('vcfR') # Documentation citation('vcfR') # Citation ***** ***** ***** ***** Registered S3 method overwritten by 'pegas': method from print.amova ade4 Registered S3 method overwritten by 'genetics': method from [.haplotype pegas > library(dartRverse) ********************************************** **** Welcome to dartRverse [Version 1.0.6] **** ********************************************** ── Core dartRverse packages ──────────────────────────────────────────────────────────────── dartRverse ── ✔ dartR.base 1.0.7 ✔ dartR.data 1.0.8 ── Installed dartRverse packages ───────────────────────────────────────────────────────── dartRverse ── ✔ dartR.popgen 1.0.5 ✔ dartR.spatial 0.92 ✔ dartR.sim 0.70 ── Not [yet] installed dartRverse packages ───────────────────────────────────────────────── dartRverse ── ✖ dartR.captive ✖ dartR.sexlinked Warning messages: 1: package ‘adegenet’ was built under R version 4.4.3 2: package ‘ade4’ was built under R version 4.4.3 3: package ‘dartRverse’ was built under R version 4.4.3 > library(dartR.popgen) > library(ggplot2) > library(devtools) Loading required package: usethis Warning message: package ‘usethis’ was built under R version 4.4.3 > library(geohippos) Loading required package: parallel Loading required package: furrr Loading required package: future Attaching package: ‘geohippos’ The following object is masked from ‘package:dartR.base’: gl.read.vcf Warning message: package ‘future’ was built under R version 4.4.3 > # Run as it was classically run > # SNP data (use two populations and only the first 100 SNPs)
> pops <- possums.gl[1:60, 1:100]
> nes <- gl.LDNe(pops, outfile = "popsLD.txt", neest.path = "./Ne/",
+ critical = c(0, 0.05), singleton.rm = TRUE, mating = "random")
Starting gl.LDNe
Processing genlight object with SNP data
Starting gl2genepop
Processing genlight object with SNP data
The genepop file is saved as: C:\Users\YAYANK~1\AppData\Local\Temp\RtmpQNzEH6/dummy.gen/
Completed: gl2genepop
Number of loci = 100, 2-digit alleles
Input file: dummy.gen - GENEPOP format
Number of loci = 100, 2-digit alleles
Method(s): LD
Locus names - last 6 characters:
X1 X2 X3 X4 X5 X6 X7 X8 X9 X10
X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
X21 X22 X23 X24 X25 X26 X27 X28 X29 X30
X31 X32 X33 X34 X35 X36 X37 X38 X39 X40
X41 X42 X43 X44 X45 X46 X47 X48 X49 X50
X51 X52 X53 X54 X55 X56 X57 X58 X59 X60
X61 X62 X63 X64 X65 X66 X67 X68 X69 X70
X71 X72 X73 X74 X75 X76 X77 X78 X79 X80
X81 X82 X83 X84 X85 X86 X87 X88 X89 X90
X91 X92 X93 X94 X95 X96 X97 X98 X99 X100
Outputs are written to file popsLD.txt
Tabular-format LD Output File Name: popsLDxLD.txt
Starting time: Thu Oct 23 10:34:17 2025
Population 1 [A_1]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 14.3
Parameter CI: 12.1 16.9
Jackknife CI: 8.6 24.7
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
* For lowest freq: 0.000
Estimate of Ne: 15.1
Parameter CI: 12.9 17.7
Jackknife CI: 9.8 24.1
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
Population 2 [B_31]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
* For lowest freq: 0.000
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
Error in `levels<-`(`*tmp*`, value = as.character(levels)) :
factor level [2] is duplicated
> # Error in `levels<-`(`*tmp*`, value = as.character(levels)) : factor level [2] is duplicated
> # emerge
> indNames(pops) <- make.unique(indNames(pops)) #add .1 etc to duplicates
> nes <- gl.LDNe(pops, outfile = "popsLD.txt", neest.path = "./Ne/",
+ critical = c(0, 0.05), singleton.rm = TRUE, mating = "random")
Starting gl.LDNe
Processing genlight object with SNP data
Starting gl2genepop
Processing genlight object with SNP data
The genepop file is saved as: C:\Users\YAYANK~1\AppData\Local\Temp\RtmpQNzEH6/dummy.gen/
Completed: gl2genepop
Number of loci = 100, 2-digit alleles
Input file: dummy.gen - GENEPOP format
Number of loci = 100, 2-digit alleles
Method(s): LD
Locus names - last 6 characters:
X1 X2 X3 X4 X5 X6 X7 X8 X9 X10
X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
X21 X22 X23 X24 X25 X26 X27 X28 X29 X30
X31 X32 X33 X34 X35 X36 X37 X38 X39 X40
X41 X42 X43 X44 X45 X46 X47 X48 X49 X50
X51 X52 X53 X54 X55 X56 X57 X58 X59 X60
X61 X62 X63 X64 X65 X66 X67 X68 X69 X70
X71 X72 X73 X74 X75 X76 X77 X78 X79 X80
X81 X82 X83 X84 X85 X86 X87 X88 X89 X90
X91 X92 X93 X94 X95 X96 X97 X98 X99 X100
Outputs are written to file popsLD.txt
Tabular-format LD Output File Name: popsLDxLD.txt
Starting time: Thu Oct 23 10:35:26 2025
Population 1 [A_1]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 14.3
Parameter CI: 12.1 16.9
Jackknife CI: 8.6 24.7
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
* For lowest freq: 0.000
Estimate of Ne: 15.1
Parameter CI: 12.9 17.7
Jackknife CI: 9.8 24.1
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
Population 2 [B_31]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
* For lowest freq: 0.000
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
Error in `levels<-`(`*tmp*`, value = as.character(levels)) :
factor level [2] is duplicated
> #and potentially also
> locNames(pops) <- make.unique(locNames(pops))
> nes <- gl.LDNe(pops, outfile = "popsLD.txt", neest.path = "./Ne/",
+ critical = c(0, 0.05), singleton.rm = TRUE, mating = "random")
Starting gl.LDNe
Processing genlight object with SNP data
Starting gl2genepop
Processing genlight object with SNP data
The genepop file is saved as: C:\Users\YAYANK~1\AppData\Local\Temp\RtmpQNzEH6/dummy.gen/
Completed: gl2genepop
Number of loci = 100, 2-digit alleles
Input file: dummy.gen - GENEPOP format
Number of loci = 100, 2-digit alleles
Method(s): LD
Locus names - last 6 characters:
X1 X2 X3 X4 X5 X6 X7 X8 X9 X10
X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
X21 X22 X23 X24 X25 X26 X27 X28 X29 X30
X31 X32 X33 X34 X35 X36 X37 X38 X39 X40
X41 X42 X43 X44 X45 X46 X47 X48 X49 X50
X51 X52 X53 X54 X55 X56 X57 X58 X59 X60
X61 X62 X63 X64 X65 X66 X67 X68 X69 X70
X71 X72 X73 X74 X75 X76 X77 X78 X79 X80
X81 X82 X83 X84 X85 X86 X87 X88 X89 X90
X91 X92 X93 X94 X95 X96 X97 X98 X99 X100
Outputs are written to file popsLD.txt
Tabular-format LD Output File Name: popsLDxLD.txt
Starting time: Thu Oct 23 10:35:35 2025
Population 1 [A_1]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 14.3
Parameter CI: 12.1 16.9
Jackknife CI: 8.6 24.7
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
* For lowest freq: 0.000
Estimate of Ne: 15.1
Parameter CI: 12.9 17.7
Jackknife CI: 9.8 24.1
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
Population 2 [B_31]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
* For lowest freq: 0.000
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
Error in `levels<-`(`*tmp*`, value = as.character(levels)) :
factor level [2] is duplicated
> pops@pop [1] A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A B B B B B B B B B B B B B B B B B B B B B [52] B B B B B B B B B Levels: A B > indNames(pops) [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" [21] "21" "22" "23" "24" "25" "26" "27" "28" "29" "30" "31" "32" "33" "34" "35" "36" "37" "38" "39" "40" [41] "41" "42" "43" "44" "45" "46" "47" "48" "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" "60" > locNames(pops) [1] "X1" "X2" "X3" "X4" "X5" "X6" "X7" "X8" "X9" "X10" "X11" "X12" "X13" "X14" [15] "X15" "X16" "X17" "X18" "X19" "X20" "X21" "X22" "X23" "X24" "X25" "X26" "X27" "X28" [29] "X29" "X30" "X31" "X32" "X33" "X34" "X35" "X36" "X37" "X38" "X39" "X40" "X41" "X42" [43] "X43" "X44" "X45" "X46" "X47" "X48" "X49" "X50" "X51" "X52" "X53" "X54" "X55" "X56" [57] "X57" "X58" "X59" "X60" "X61" "X62" "X63" "X64" "X65" "X66" "X67" "X68" "X69" "X70" [71] "X71" "X72" "X73" "X74" "X75" "X76" "X77" "X78" "X79" "X80" "X81" "X82" "X83" "X84" [85] "X85" "X86" "X87" "X88" "X89" "X90" "X91" "X92" "X93" "X94" "X95" "X96" "X97" "X98" [99] "X99" "X100" > pops /// GENLIGHT OBJECT ///////// // 60 genotypes, 100 binary SNPs, size: 129.4 Kb 0 (0 %) missing data // Basic content @gen: list of 60 SNPbin @ploidy: ploidy of each individual (range: 2-2) // Optional content @ind.names: 60 individual labels @loc.names: 100 locus labels @pop: population of each individual (group size range: 30-30) @other: a list containing: xy loc.metrics loc.metrics.flags verbose history latlon > # still doesn't work > pop(pops) <- make.unique(pop(pops)) Error in make.unique(pop(pops)) : 'names' must be a character vector > # still doesn't work > popNames(pops) <- make.unique(popNames(pops)) > pops@pop [1] A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A B B B B B B B B B B B B B B B B B B B B B [52] B B B B B B B B B Levels: A B
> nes <- gl.LDNe(pops, outfile = "popsLD.txt", neest.path = "./Ne/",
+ critical = c(0, 0.05), singleton.rm = TRUE, mating = "random")
Starting gl.LDNe
Processing genlight object with SNP data
Starting gl2genepop
Processing genlight object with SNP data
The genepop file is saved as: C:\Users\YAYANK~1\AppData\Local\Temp\RtmpQNzEH6/dummy.gen/
Completed: gl2genepop
Number of loci = 100, 2-digit alleles
Input file: dummy.gen - GENEPOP format
Number of loci = 100, 2-digit alleles
Method(s): LD
Locus names - last 6 characters:
X1 X2 X3 X4 X5 X6 X7 X8 X9 X10
X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
X21 X22 X23 X24 X25 X26 X27 X28 X29 X30
X31 X32 X33 X34 X35 X36 X37 X38 X39 X40
X41 X42 X43 X44 X45 X46 X47 X48 X49 X50
X51 X52 X53 X54 X55 X56 X57 X58 X59 X60
X61 X62 X63 X64 X65 X66 X67 X68 X69 X70
X71 X72 X73 X74 X75 X76 X77 X78 X79 X80
X81 X82 X83 X84 X85 X86 X87 X88 X89 X90
X91 X92 X93 X94 X95 X96 X97 X98 X99 X100
Outputs are written to file popsLD.txt
Tabular-format LD Output File Name: popsLDxLD.txt
Starting time: Thu Oct 23 10:38:24 2025
Population 1 [A_1]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 14.3
Parameter CI: 12.1 16.9
Jackknife CI: 8.6 24.7
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
* For lowest freq: 0.000
Estimate of Ne: 15.1
Parameter CI: 12.9 17.7
Jackknife CI: 9.8 24.1
* For lowest freq: 0+
Estimate of Ne: 15.9
Parameter CI: 13.6 18.7
Jackknife CI: 10.4 25.6
Population 2 [B_31]
-> Total samples = 30
Allele frequencies are being written to file dummyLoc.txt.
* For lowest freq: 0.050
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
* For lowest freq: 0.000
Estimate of Ne: 17.1
Parameter CI: 14.7 19.9
Jackknife CI: 11.5 26.5
* For lowest freq: 0+
Estimate of Ne: 18.5
Parameter CI: 16.0 21.6
Jackknife CI: 12.3 29.6
Error in `levels<-`(`*tmp*`, value = as.character(levels)) :
factor level [2] is duplicated
> pops /// GENLIGHT OBJECT ///////// // 60 genotypes, 100 binary SNPs, size: 129.4 Kb 0 (0 %) missing data // Basic content @gen: list of 60 SNPbin @ploidy: ploidy of each individual (range: 2-2) // Optional content @ind.names: 60 individual labels @loc.names: 100 locus labels @pop: population of each individual (group size range: 30-30) @other: a list containing: xy loc.metrics loc.metrics.flags verbose history latlon > # Run as it was classically run > # SNP data (use two populations and only the first 100 SNPs)
> pops <- possums.gl[1:60, 1:100]
> pops /// GENLIGHT OBJECT ///////// // 60 genotypes, 100 binary SNPs, size: 129.4 Kb 0 (0 %) missing data // Basic content @gen: list of 60 SNPbin @ploidy: ploidy of each individual (range: 2-2) // Optional content @ind.names: 60 individual labels @loc.names: 100 locus labels @pop: population of each individual (group size range: 30-30) @other: a list containing: xy loc.metrics loc.metrics.flags verbose history latlon > po...@ind.names [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" [21] "21" "22" "23" "24" "25" "26" "27" "28" "29" "30" "31" "32" "33" "34" "35" "36" "37" "38" "39" "40" [41] "41" "42" "43" "44" "45" "46" "47" "48" "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" "60" > po...@loc.names [1] "X1" "X2" "X3" "X4" "X5" "X6" "X7" "X8" "X9" "X10" "X11" "X12" "X13" "X14" [15] "X15" "X16" "X17" "X18" "X19" "X20" "X21" "X22" "X23" "X24" "X25" "X26" "X27" "X28" [29] "X29" "X30" "X31" "X32" "X33" "X34" "X35" "X36" "X37" "X38" "X39" "X40" "X41" "X42" [43] "X43" "X44" "X45" "X46" "X47" "X48" "X49" "X50" "X51" "X52" "X53" "X54" "X55" "X56" [57] "X57" "X58" "X59" "X60" "X61" "X62" "X63" "X64" "X65" "X66" "X67" "X68" "X69" "X70" [71] "X71" "X72" "X73" "X74" "X75" "X76" "X77" "X78" "X79" "X80" "X81" "X82" "X83" "X84" [85] "X85" "X86" "X87" "X88" "X89" "X90" "X91" "X92" "X93" "X94" "X95" "X96" "X97" "X98" [99] "X99" "X100" > pop(pops) <- make.unique(pop(pops)) Error in make.unique(pop(pops)) : 'names' must be a character vector
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