Last updated on 2024-12-23 12:49:25 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 1.4.1 | 15.77 | 505.34 | 521.11 | OK | |
r-devel-linux-x86_64-debian-gcc | 1.4.1 | 10.84 | 270.16 | 281.00 | OK | |
r-devel-linux-x86_64-fedora-clang | 1.4.1 | 778.85 | OK | |||
r-devel-linux-x86_64-fedora-gcc | 1.4.1 | 779.68 | OK | |||
r-devel-windows-x86_64 | 1.4.1 | 123.00 | 543.00 | 666.00 | ERROR | |
r-patched-linux-x86_64 | 1.4.1 | 15.07 | 446.65 | 461.72 | OK | |
r-release-linux-x86_64 | 1.4.1 | 14.72 | 427.17 | 441.89 | OK | |
r-release-macos-arm64 | 1.4.1 | 306.00 | OK | |||
r-release-macos-x86_64 | 1.4.1 | 903.00 | OK | |||
r-release-windows-x86_64 | 1.4.1 | 128.00 | 534.00 | 662.00 | ERROR | |
r-oldrel-macos-arm64 | 1.4.1 | 305.00 | OK | |||
r-oldrel-macos-x86_64 | 1.4.1 | 917.00 | OK | |||
r-oldrel-windows-x86_64 | 1.4.1 | 129.00 | 649.00 | 778.00 | ERROR |
Version: 1.4.1
Check: examples
Result: ERROR
Running examples in 'SFSI-Ex.R' failed
The error most likely occurred in:
> ### Name: Reading and combining SGP outputs
> ### Title: Read and combine SGP outputs
> ### Aliases: read_SGP read_summary
>
> ### ** Examples
>
> require(SFSI)
> data(wheatHTP)
>
> index = which(Y$trial %in% 1:10) # Use only a subset of data
> Y = Y[index,]
> M = scale(M[index,])/sqrt(ncol(M)) # Subset and scale markers
> G = tcrossprod(M) # Genomic relationship matrix
> y = as.vector(scale(Y[,"E1"])) # Scale response variable
>
> # Training and testing sets
> tst = which(Y$trial %in% 1:3)
> trn = seq_along(y)[-tst]
>
> path = paste0(tempdir(),"/testSGP_")
>
> # Run the analysis into 4 subsets and save them at a given path
> SGP(y, K=G, trn=trn, tst=tst, subset=c(1,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 1/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_18_01_50_01_11818\RtmpQ5XJJ7\testSGP_subset_1_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(2,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 2/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_18_01_50_01_11818\RtmpQ5XJJ7\testSGP_subset_2_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(3,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 3/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_18_01_50_01_11818\RtmpQ5XJJ7\testSGP_subset_3_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(4,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 4/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_18_01_50_01_11818\RtmpQ5XJJ7\testSGP_subset_4_of_4_SGP.RData'
>
> # Collect all results after completion
> fm = read_SGP(path)
Warning in grep(pattern = paste0(fullpath, "$"), value = TRUE, x = list.files(infolder, :
TRE pattern compilation error 'Invalid back reference'
Error in grep(pattern = paste0(fullpath, "$"), value = TRUE, x = list.files(infolder, :
invalid regular expression 'D:\temp\2024_12_18_01_50_01_11818\RtmpQ5XJJ7\testSGP_.*SGP.RData$', reason 'Invalid back reference'
Calls: read_SGP -> lapply -> FUN -> basename -> grep
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.4.1
Check: examples
Result: ERROR
Running examples in 'SFSI-Ex.R' failed
The error most likely occurred in:
> ### Name: Reading and combining SGP outputs
> ### Title: Read and combine SGP outputs
> ### Aliases: read_SGP read_summary
>
> ### ** Examples
>
> require(SFSI)
> data(wheatHTP)
>
> index = which(Y$trial %in% 1:10) # Use only a subset of data
> Y = Y[index,]
> M = scale(M[index,])/sqrt(ncol(M)) # Subset and scale markers
> G = tcrossprod(M) # Genomic relationship matrix
> y = as.vector(scale(Y[,"E1"])) # Scale response variable
>
> # Training and testing sets
> tst = which(Y$trial %in% 1:3)
> trn = seq_along(y)[-tst]
>
> path = paste0(tempdir(),"/testSGP_")
>
> # Run the analysis into 4 subsets and save them at a given path
> SGP(y, K=G, trn=trn, tst=tst, subset=c(1,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 1/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_08_01_50_01_8405\RtmpwjiLqZ\testSGP_subset_1_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(2,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 2/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_08_01_50_01_8405\RtmpwjiLqZ\testSGP_subset_2_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(3,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 3/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_08_01_50_01_8405\RtmpwjiLqZ\testSGP_subset_3_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(4,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 4/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_08_01_50_01_8405\RtmpwjiLqZ\testSGP_subset_4_of_4_SGP.RData'
>
> # Collect all results after completion
> fm = read_SGP(path)
Warning in grep(pattern = paste0(fullpath, "$"), value = TRUE, x = list.files(infolder, :
TRE pattern compilation error 'Invalid back reference'
Error in grep(pattern = paste0(fullpath, "$"), value = TRUE, x = list.files(infolder, :
invalid regular expression 'D:\temp\2024_12_08_01_50_01_8405\RtmpwjiLqZ\testSGP_.*SGP.RData$', reason 'Invalid back reference'
Calls: read_SGP -> lapply -> FUN -> basename -> grep
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.4.1
Check: examples
Result: ERROR
Running examples in 'SFSI-Ex.R' failed
The error most likely occurred in:
> ### Name: Reading and combining SGP outputs
> ### Title: Read and combine SGP outputs
> ### Aliases: read_SGP read_summary
>
> ### ** Examples
>
> require(SFSI)
> data(wheatHTP)
>
> index = which(Y$trial %in% 1:10) # Use only a subset of data
> Y = Y[index,]
> M = scale(M[index,])/sqrt(ncol(M)) # Subset and scale markers
> G = tcrossprod(M) # Genomic relationship matrix
> y = as.vector(scale(Y[,"E1"])) # Scale response variable
>
> # Training and testing sets
> tst = which(Y$trial %in% 1:3)
> trn = seq_along(y)[-tst]
>
> path = paste0(tempdir(),"/testSGP_")
>
> # Run the analysis into 4 subsets and save them at a given path
> SGP(y, K=G, trn=trn, tst=tst, subset=c(1,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 1/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_20_01_50_00_19051\Rtmp2vdAVO\testSGP_subset_1_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(2,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 2/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_20_01_50_00_19051\Rtmp2vdAVO\testSGP_subset_2_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(3,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 3/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_20_01_50_00_19051\Rtmp2vdAVO\testSGP_subset_3_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(4,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 4/4) of 84 and nTRN = 194 records
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Results were saved at file:
'D:\temp\2024_12_20_01_50_00_19051\Rtmp2vdAVO\testSGP_subset_4_of_4_SGP.RData'
>
> # Collect all results after completion
> fm = read_SGP(path)
Warning in grep(pattern = paste0(fullpath, "$"), value = TRUE, x = list.files(infolder, :
TRE pattern compilation error 'Invalid back reference'
Error in grep(pattern = paste0(fullpath, "$"), value = TRUE, x = list.files(infolder, :
invalid regular expression 'D:\temp\2024_12_20_01_50_00_19051\Rtmp2vdAVO\testSGP_.*SGP.RData$', reason 'Invalid back reference'
Calls: read_SGP -> lapply -> FUN -> basename -> grep
Execution halted
Flavor: r-oldrel-windows-x86_64