Last updated on 2025-08-09 05:49:10 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| GRAB | 4 | 2 | 7 |
Current CRAN status: ERROR: 4, NOTE: 2, OK: 7
Version: 0.2.2
Check: examples
Result: ERROR
Running examples in ‘GRAB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GRAB.POLMM
> ### Title: POLMM method in GRAB package
> ### Aliases: GRAB.POLMM
>
> ### ** Examples
>
> ### First, Read Data and Convert Phenotype to a Factor
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> PhenoFile <- system.file("extdata", "simuPHENO.txt", package = "GRAB")
> PhenoData <- data.table::fread(PhenoFile, header = TRUE)
> PhenoData <- PhenoData %>% mutate(OrdinalPheno = factor(OrdinalPheno,
+ levels = c(0, 1, 2)
+ ))
>
> ### Step 1: Fit a null model
> # If a sparse GRM is used in model fitting, SparseGRMFile is required.
> # If SparseGRMFile isn't provided, GRAB.NullModel() will calculate dense GRM from GenoFile.
>
> SparseGRMFile <- system.file("SparseGRM", "SparseGRM.txt", package = "GRAB")
> GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")
> obj.POLMM <- GRAB.NullModel(
+ formula = OrdinalPheno ~ AGE + GENDER,
+ data = PhenoData,
+ subjData = PhenoData$IID,
+ method = "POLMM",
+ traitType = "ordinal",
+ GenoFile = GenoFile,
+ SparseGRMFile = SparseGRMFile,
+ control = list(
+ showInfo = FALSE,
+ LOCO = FALSE,
+ tolTau = 0.2,
+ tolBeta = 0.1
+ )
+ )
Number of subjects in 'formula': 1000
Reading bim file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/GRAB/extdata/simuPLINK.bim
Reading fam file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/GRAB/extdata/simuPLINK.fam
setting PLINK object in CPP....
Reading bim file....
Reading fam file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/GRAB/extdata/simuPLINK.fam
m_N: 1000
Setting position of samples in PLINK files....
posSampleInPlink: 501 510 600
SampleInModel: Subj-1 Subj-10 Subj-100
SampleInPlink: f1_1 f1_2 f1_3
Number of samples: 1000
Based on the 'GenoFile' and 'GenoFileIndex',PLINKformat is used for genotype data.
Sparse GRM is used when fitting a null model.
The below are the list of control parameters used in null model fitting.
2-1301000.10.20.21001e-061001e-100.10.1200.0025auto10.010.1FALSEFALSEFALSE
gIndex: 1016
gIndex: 678
gIndex: 128
gIndex: 929
gIndex: 470
gIndex: 298
gIndex: 269
gIndex: 596
gIndex: 329
gIndex: 36
gIndex: 728
gIndex: 877
gIndex: 484
gIndex: 873
gIndex: 381
gIndex: 974
gIndex: 800
gIndex: 851
gIndex: 930
gIndex: 325
gIndex: 1091
gIndex: 553
gIndex: 110
gIndex: 531
gIndex: 555
gIndex: 888
gIndex: 342
gIndex: 581
gIndex: 39
gIndex: 536
gIndex: 374
gIndex: 247
gIndex: 377
gIndex: 38
gIndex: 434
gIndex: 809
gIndex: 525
gIndex: 641
gIndex: 21
gIndex: 192
gIndex: 498
gIndex: 982
gIndex: 842
gIndex: 464
gIndex: 995
gIndex: 83
gIndex: 1052
gIndex: 251
gIndex: 732
gIndex: 619
gIndex: 556
gIndex: 286
gIndex: 613
gIndex: 328
gIndex: 486
gIndex: 854
gIndex: 850
gIndex: 857
gIndex: 618
gIndex: 575
gIndex: 989
gIndex: 1022
gIndex: 315
gIndex: 1051
gIndex: 649
gIndex: 1097
gIndex: 810
gIndex: 954
gIndex: 281
gIndex: 284
gIndex: 500
gIndex: 510
gIndex: 535
gIndex: 692
gIndex: 987
gIndex: 736
gIndex: 338
gIndex: 345
gIndex: 674
gIndex: 42
gIndex: 0
gIndex: 28
gIndex: 589
gIndex: 917
gIndex: 837
gIndex: 795
gIndex: 627
gIndex: 232
gIndex: 292
gIndex: 572
gIndex: 941
gIndex: 368
gIndex: 450
gIndex: 85
gIndex: 482
gIndex: 326
gIndex: 621
gIndex: 354
gIndex: 818
gIndex: 811
gIndex: 48
gIndex: 360
gIndex: 1037
gIndex: 241
gIndex: 439
gIndex: 757
gIndex: 816
gIndex: 817
gIndex: 246
gIndex: 750
gIndex: 218
gIndex: 134
It took 0.003075 seconds (0.003074 CPU seconds) to calculate 30 genKinbVec().
Start iteration .....
d2eps: -1.3071e+02
d1eps: 2.7770
deps: 0.0212
iter: 0
m_eps: 0
0.9821
eps0: 0
0.9609
m_tolEps: 1e-10
d2eps: -1.2536e+02
d1eps: 0.0574
deps: 0.0005
iter: 1
m_eps: 0
0.9826
eps0: 0
0.9821
m_tolEps: 1e-10
d2eps: -1.2525e+02
d1eps: 2.5614e-05
deps: 2.0451e-07
iter: 2
m_eps: 0
0.9826
eps0: 0
0.9826
m_tolEps: 1e-10
d2eps: -1.2525e+02
d1eps: 5.0837e-12
deps: 4.0590e-14
iter: 3
m_eps: 0
0.9826
eps0: 0
0.9826
m_tolEps: 1e-10
UpdateEps iter: 3
eps:
0
0.9826
beta:
-37.5557
0.5975
0.3791
diffBeta: 0.00275036
Start updating tau...
iter: 0
beta:
-37.5557
0.5975
0.3791
tau: 0.0293943
d2eps: -1.2360e+02
d1eps: -2.2300
deps: -0.0180
iter: 0
m_eps: 0
0.9646
eps0: 0
0.9826
m_tolEps: 1e-10
d2eps: -1.2811e+02
d1eps: 0.0403
deps: 0.0003
iter: 1
m_eps: 0
0.9649
eps0: 0
0.9646
m_tolEps: 1e-10
d2eps: -1.2803e+02
d1eps: 1.2656e-05
deps: 9.8853e-08
iter: 2
m_eps: 0
0.9649
eps0: 0
0.9649
m_tolEps: 1e-10
d2eps: -1.2803e+02
d1eps: 1.2440e-12
deps: 9.7169e-15
iter: 3
m_eps: 0
0.9649
eps0: 0
0.9649
m_tolEps: 1e-10
UpdateEps iter: 3
eps:
0
0.9649
beta:
-37.5479
0.5974
0.3811
diffBeta: 0.00231347
Start updating tau...
iter: 1
beta:
-37.5479
0.5974
0.3811
tau: 0.0136161
It took 0.070414 seconds (0.070407 CPU seconds) to fit the null POLMM..
Start estimating variance ratio....
nSNPs for CV: 20
CV: 5.84339e-06
Complete the null model fitting in package GRAB: Complete Time: 2025-08-07 17:15:58.789623
>
> objPOLMMFile <- system.file("results", "objPOLMMFile.RData", package = "GRAB")
> save(obj.POLMM, file = objPOLMMFile)
Warning in gzfile(file, "wb") :
cannot open compressed file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/GRAB/results/objPOLMMFile.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: save -> gzfile
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.2
Check: examples
Result: ERROR
Running examples in ‘GRAB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GRAB.POLMM
> ### Title: POLMM method in GRAB package
> ### Aliases: GRAB.POLMM
>
> ### ** Examples
>
> ### First, Read Data and Convert Phenotype to a Factor
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> PhenoFile <- system.file("extdata", "simuPHENO.txt", package = "GRAB")
> PhenoData <- data.table::fread(PhenoFile, header = TRUE)
> PhenoData <- PhenoData %>% mutate(OrdinalPheno = factor(OrdinalPheno,
+ levels = c(0, 1, 2)
+ ))
>
> ### Step 1: Fit a null model
> # If a sparse GRM is used in model fitting, SparseGRMFile is required.
> # If SparseGRMFile isn't provided, GRAB.NullModel() will calculate dense GRM from GenoFile.
>
> SparseGRMFile <- system.file("SparseGRM", "SparseGRM.txt", package = "GRAB")
> GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")
> obj.POLMM <- GRAB.NullModel(
+ formula = OrdinalPheno ~ AGE + GENDER,
+ data = PhenoData,
+ subjData = PhenoData$IID,
+ method = "POLMM",
+ traitType = "ordinal",
+ GenoFile = GenoFile,
+ SparseGRMFile = SparseGRMFile,
+ control = list(
+ showInfo = FALSE,
+ LOCO = FALSE,
+ tolTau = 0.2,
+ tolBeta = 0.1
+ )
+ )
Number of subjects in 'formula': 1000
Reading bim file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.bim
Reading fam file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
setting PLINK object in CPP....
Reading bim file....
Reading fam file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
m_N: 1000
Setting position of samples in PLINK files....
posSampleInPlink: 501 510 600
SampleInModel: Subj-1 Subj-10 Subj-100
SampleInPlink: f1_1 f1_2 f1_3
Number of samples: 1000
Based on the 'GenoFile' and 'GenoFileIndex',PLINKformat is used for genotype data.
Sparse GRM is used when fitting a null model.
The below are the list of control parameters used in null model fitting.
2-1301000.10.20.21001e-061001e-100.10.1200.0025auto10.010.1FALSEFALSEFALSE
gIndex: 1016
gIndex: 678
gIndex: 128
gIndex: 929
gIndex: 470
gIndex: 298
gIndex: 269
gIndex: 596
gIndex: 329
gIndex: 36
gIndex: 728
gIndex: 877
gIndex: 484
gIndex: 873
gIndex: 381
gIndex: 974
gIndex: 800
gIndex: 851
gIndex: 930
gIndex: 325
gIndex: 1091
gIndex: 553
gIndex: 110
gIndex: 531
gIndex: 555
gIndex: 888
gIndex: 342
gIndex: 581
gIndex: 39
gIndex: 536
gIndex: 374
gIndex: 247
gIndex: 377
gIndex: 38
gIndex: 434
gIndex: 809
gIndex: 525
gIndex: 641
gIndex: 21
gIndex: 192
gIndex: 498
gIndex: 982
gIndex: 842
gIndex: 464
gIndex: 995
gIndex: 83
gIndex: 1052
gIndex: 251
gIndex: 732
gIndex: 619
gIndex: 556
gIndex: 286
gIndex: 613
gIndex: 328
gIndex: 486
gIndex: 854
gIndex: 850
gIndex: 857
gIndex: 618
gIndex: 575
gIndex: 989
gIndex: 1022
gIndex: 315
gIndex: 1051
gIndex: 649
gIndex: 1097
gIndex: 810
gIndex: 954
gIndex: 281
gIndex: 284
gIndex: 500
gIndex: 510
gIndex: 535
gIndex: 692
gIndex: 987
gIndex: 736
gIndex: 338
gIndex: 345
gIndex: 674
gIndex: 42
gIndex: 0
gIndex: 28
gIndex: 589
gIndex: 917
gIndex: 837
gIndex: 795
gIndex: 627
gIndex: 232
gIndex: 292
gIndex: 572
gIndex: 941
gIndex: 368
gIndex: 450
gIndex: 85
gIndex: 482
gIndex: 326
gIndex: 621
gIndex: 354
gIndex: 818
gIndex: 811
gIndex: 48
gIndex: 360
gIndex: 1037
gIndex: 241
gIndex: 439
gIndex: 757
gIndex: 816
gIndex: 817
gIndex: 246
gIndex: 750
gIndex: 218
gIndex: 134
It took 0.002471 seconds (0.002468 CPU seconds) to calculate 30 genKinbVec().
Start iteration .....
d2eps: -1.3071e+02
d1eps: 2.7770
deps: 0.0212
iter: 0
m_eps: 0
0.9821
eps0: 0
0.9609
m_tolEps: 1e-10
d2eps: -1.2536e+02
d1eps: 0.0574
deps: 0.0005
iter: 1
m_eps: 0
0.9826
eps0: 0
0.9821
m_tolEps: 1e-10
d2eps: -1.2525e+02
d1eps: 2.5614e-05
deps: 2.0451e-07
iter: 2
m_eps: 0
0.9826
eps0: 0
0.9826
m_tolEps: 1e-10
d2eps: -1.2525e+02
d1eps: 5.0837e-12
deps: 4.0590e-14
iter: 3
m_eps: 0
0.9826
eps0: 0
0.9826
m_tolEps: 1e-10
UpdateEps iter: 3
eps:
0
0.9826
beta:
-37.5557
0.5975
0.3791
diffBeta: 0.00275036
Start updating tau...
iter: 0
beta:
-37.5557
0.5975
0.3791
tau: 0.0293943
d2eps: -1.2360e+02
d1eps: -2.2300
deps: -0.0180
iter: 0
m_eps: 0
0.9646
eps0: 0
0.9826
m_tolEps: 1e-10
d2eps: -1.2811e+02
d1eps: 0.0403
deps: 0.0003
iter: 1
m_eps: 0
0.9649
eps0: 0
0.9646
m_tolEps: 1e-10
d2eps: -1.2803e+02
d1eps: 1.2656e-05
deps: 9.8853e-08
iter: 2
m_eps: 0
0.9649
eps0: 0
0.9649
m_tolEps: 1e-10
d2eps: -1.2803e+02
d1eps: 1.2440e-12
deps: 9.7169e-15
iter: 3
m_eps: 0
0.9649
eps0: 0
0.9649
m_tolEps: 1e-10
UpdateEps iter: 3
eps:
0
0.9649
beta:
-37.5479
0.5974
0.3811
diffBeta: 0.00231347
Start updating tau...
iter: 1
beta:
-37.5479
0.5974
0.3811
tau: 0.0136161
It took 0.042828 seconds (0.041628 CPU seconds) to fit the null POLMM..
Start estimating variance ratio....
nSNPs for CV: 20
CV: 5.84339e-06
Complete the null model fitting in package GRAB: Complete Time: 2025-08-08 13:19:11.500123
>
> objPOLMMFile <- system.file("results", "objPOLMMFile.RData", package = "GRAB")
> save(obj.POLMM, file = objPOLMMFile)
Warning in gzfile(file, "wb") :
cannot open compressed file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/results/objPOLMMFile.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: save -> gzfile
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.2
Check: examples
Result: ERROR
Running examples in ‘GRAB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GRAB.POLMM
> ### Title: POLMM method in GRAB package
> ### Aliases: GRAB.POLMM
>
> ### ** Examples
>
> ### First, Read Data and Convert Phenotype to a Factor
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> PhenoFile <- system.file("extdata", "simuPHENO.txt", package = "GRAB")
> PhenoData <- data.table::fread(PhenoFile, header = TRUE)
> PhenoData <- PhenoData %>% mutate(OrdinalPheno = factor(OrdinalPheno,
+ levels = c(0, 1, 2)
+ ))
>
> ### Step 1: Fit a null model
> # If a sparse GRM is used in model fitting, SparseGRMFile is required.
> # If SparseGRMFile isn't provided, GRAB.NullModel() will calculate dense GRM from GenoFile.
>
> SparseGRMFile <- system.file("SparseGRM", "SparseGRM.txt", package = "GRAB")
> GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")
> obj.POLMM <- GRAB.NullModel(
+ formula = OrdinalPheno ~ AGE + GENDER,
+ data = PhenoData,
+ subjData = PhenoData$IID,
+ method = "POLMM",
+ traitType = "ordinal",
+ GenoFile = GenoFile,
+ SparseGRMFile = SparseGRMFile,
+ control = list(
+ showInfo = FALSE,
+ LOCO = FALSE,
+ tolTau = 0.2,
+ tolBeta = 0.1
+ )
+ )
Number of subjects in 'formula': 1000
Reading bim file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.bim
Reading fam file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
setting PLINK object in CPP....
Reading bim file....
Reading fam file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
m_N: 1000
Setting position of samples in PLINK files....
posSampleInPlink: 501 510 600
SampleInModel: Subj-1 Subj-10 Subj-100
SampleInPlink: f1_1 f1_2 f1_3
Number of samples: 1000
Based on the 'GenoFile' and 'GenoFileIndex',PLINKformat is used for genotype data.
Sparse GRM is used when fitting a null model.
The below are the list of control parameters used in null model fitting.
2-1301000.10.20.21001e-061001e-100.10.1200.0025auto10.010.1FALSEFALSEFALSE
gIndex: 1016
gIndex: 678
gIndex: 128
gIndex: 929
gIndex: 470
gIndex: 298
gIndex: 269
gIndex: 596
gIndex: 329
gIndex: 36
gIndex: 728
gIndex: 877
gIndex: 484
gIndex: 873
gIndex: 381
gIndex: 974
gIndex: 800
gIndex: 851
gIndex: 930
gIndex: 325
gIndex: 1091
gIndex: 553
gIndex: 110
gIndex: 531
gIndex: 555
gIndex: 888
gIndex: 342
gIndex: 581
gIndex: 39
gIndex: 536
gIndex: 374
gIndex: 247
gIndex: 377
gIndex: 38
gIndex: 434
gIndex: 809
gIndex: 525
gIndex: 641
gIndex: 21
gIndex: 192
gIndex: 498
gIndex: 982
gIndex: 842
gIndex: 464
gIndex: 995
gIndex: 83
gIndex: 1052
gIndex: 251
gIndex: 732
gIndex: 619
gIndex: 556
gIndex: 286
gIndex: 613
gIndex: 328
gIndex: 486
gIndex: 854
gIndex: 850
gIndex: 857
gIndex: 618
gIndex: 575
gIndex: 989
gIndex: 1022
gIndex: 315
gIndex: 1051
gIndex: 649
gIndex: 1097
gIndex: 810
gIndex: 954
gIndex: 281
gIndex: 284
gIndex: 500
gIndex: 510
gIndex: 535
gIndex: 692
gIndex: 987
gIndex: 736
gIndex: 338
gIndex: 345
gIndex: 674
gIndex: 42
gIndex: 0
gIndex: 28
gIndex: 589
gIndex: 917
gIndex: 837
gIndex: 795
gIndex: 627
gIndex: 232
gIndex: 292
gIndex: 572
gIndex: 941
gIndex: 368
gIndex: 450
gIndex: 85
gIndex: 482
gIndex: 326
gIndex: 621
gIndex: 354
gIndex: 818
gIndex: 811
gIndex: 48
gIndex: 360
gIndex: 1037
gIndex: 241
gIndex: 439
gIndex: 757
gIndex: 816
gIndex: 817
gIndex: 246
gIndex: 750
gIndex: 218
gIndex: 134
It took 0.003503 seconds (0.003502 CPU seconds) to calculate 30 genKinbVec().
Start iteration .....
d2eps: -1.3071e+02
d1eps: 2.7770
deps: 0.0212
iter: 0
m_eps: 0
0.9821
eps0: 0
0.9609
m_tolEps: 1e-10
d2eps: -1.2536e+02
d1eps: 0.0574
deps: 0.0005
iter: 1
m_eps: 0
0.9826
eps0: 0
0.9821
m_tolEps: 1e-10
d2eps: -1.2525e+02
d1eps: 2.5614e-05
deps: 2.0451e-07
iter: 2
m_eps: 0
0.9826
eps0: 0
0.9826
m_tolEps: 1e-10
d2eps: -1.2525e+02
d1eps: 5.0837e-12
deps: 4.0590e-14
iter: 3
m_eps: 0
0.9826
eps0: 0
0.9826
m_tolEps: 1e-10
UpdateEps iter: 3
eps:
0
0.9826
beta:
-37.5557
0.5975
0.3791
diffBeta: 0.00275036
Start updating tau...
iter: 0
beta:
-37.5557
0.5975
0.3791
tau: 0.0293943
d2eps: -1.2360e+02
d1eps: -2.2300
deps: -0.0180
iter: 0
m_eps: 0
0.9646
eps0: 0
0.9826
m_tolEps: 1e-10
d2eps: -1.2811e+02
d1eps: 0.0403
deps: 0.0003
iter: 1
m_eps: 0
0.9649
eps0: 0
0.9646
m_tolEps: 1e-10
d2eps: -1.2803e+02
d1eps: 1.2656e-05
deps: 9.8853e-08
iter: 2
m_eps: 0
0.9649
eps0: 0
0.9649
m_tolEps: 1e-10
d2eps: -1.2803e+02
d1eps: 1.2440e-12
deps: 9.7169e-15
iter: 3
m_eps: 0
0.9649
eps0: 0
0.9649
m_tolEps: 1e-10
UpdateEps iter: 3
eps:
0
0.9649
beta:
-37.5479
0.5974
0.3811
diffBeta: 0.00231347
Start updating tau...
iter: 1
beta:
-37.5479
0.5974
0.3811
tau: 0.0136161
It took 0.106994 seconds (0.067012 CPU seconds) to fit the null POLMM..
Start estimating variance ratio....
nSNPs for CV: 20
CV: 5.84339e-06
Complete the null model fitting in package GRAB: Complete Time: 2025-08-06 05:31:40.248063
>
> objPOLMMFile <- system.file("results", "objPOLMMFile.RData", package = "GRAB")
> save(obj.POLMM, file = objPOLMMFile)
Warning in gzfile(file, "wb") :
cannot open compressed file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/GRAB/results/objPOLMMFile.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: save -> gzfile
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2.2
Check: examples
Result: ERROR
Running examples in ‘GRAB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GRAB.POLMM
> ### Title: POLMM method in GRAB package
> ### Aliases: GRAB.POLMM
>
> ### ** Examples
>
> ### First, Read Data and Convert Phenotype to a Factor
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> PhenoFile <- system.file("extdata", "simuPHENO.txt", package = "GRAB")
> PhenoData <- data.table::fread(PhenoFile, header = TRUE)
> PhenoData <- PhenoData %>% mutate(OrdinalPheno = factor(OrdinalPheno,
+ levels = c(0, 1, 2)
+ ))
>
> ### Step 1: Fit a null model
> # If a sparse GRM is used in model fitting, SparseGRMFile is required.
> # If SparseGRMFile isn't provided, GRAB.NullModel() will calculate dense GRM from GenoFile.
>
> SparseGRMFile <- system.file("SparseGRM", "SparseGRM.txt", package = "GRAB")
> GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")
> obj.POLMM <- GRAB.NullModel(
+ formula = OrdinalPheno ~ AGE + GENDER,
+ data = PhenoData,
+ subjData = PhenoData$IID,
+ method = "POLMM",
+ traitType = "ordinal",
+ GenoFile = GenoFile,
+ SparseGRMFile = SparseGRMFile,
+ control = list(
+ showInfo = FALSE,
+ LOCO = FALSE,
+ tolTau = 0.2,
+ tolBeta = 0.1
+ )
+ )
Number of subjects in 'formula': 1000
Reading bim file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.bim
Reading fam file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
setting PLINK object in CPP....
Reading bim file....
Reading fam file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
m_N: 1000
Setting position of samples in PLINK files....
posSampleInPlink: 501 510 600
SampleInModel: Subj-1 Subj-10 Subj-100
SampleInPlink: f1_1 f1_2 f1_3
Number of samples: 1000
Based on the 'GenoFile' and 'GenoFileIndex',PLINKformat is used for genotype data.
Sparse GRM is used when fitting a null model.
The below are the list of control parameters used in null model fitting.
2-1301000.10.20.21001e-061001e-100.10.1200.0025auto10.010.1FALSEFALSEFALSE
gIndex: 1016
gIndex: 678
gIndex: 128
gIndex: 929
gIndex: 470
gIndex: 298
gIndex: 269
gIndex: 596
gIndex: 329
gIndex: 36
gIndex: 728
gIndex: 877
gIndex: 484
gIndex: 873
gIndex: 381
gIndex: 974
gIndex: 800
gIndex: 851
gIndex: 930
gIndex: 325
gIndex: 1091
gIndex: 553
gIndex: 110
gIndex: 531
gIndex: 555
gIndex: 888
gIndex: 342
gIndex: 581
gIndex: 39
gIndex: 536
gIndex: 374
gIndex: 247
gIndex: 377
gIndex: 38
gIndex: 434
gIndex: 809
gIndex: 525
gIndex: 641
gIndex: 21
gIndex: 192
gIndex: 498
gIndex: 982
gIndex: 842
gIndex: 464
gIndex: 995
gIndex: 83
gIndex: 1052
gIndex: 251
gIndex: 732
gIndex: 619
gIndex: 556
gIndex: 286
gIndex: 613
gIndex: 328
gIndex: 486
gIndex: 854
gIndex: 850
gIndex: 857
gIndex: 618
gIndex: 575
gIndex: 989
gIndex: 1022
gIndex: 315
gIndex: 1051
gIndex: 649
gIndex: 1097
gIndex: 810
gIndex: 954
gIndex: 281
gIndex: 284
gIndex: 500
gIndex: 510
gIndex: 535
gIndex: 692
gIndex: 987
gIndex: 736
gIndex: 338
gIndex: 345
gIndex: 674
gIndex: 42
gIndex: 0
gIndex: 28
gIndex: 589
gIndex: 917
gIndex: 837
gIndex: 795
gIndex: 627
gIndex: 232
gIndex: 292
gIndex: 572
gIndex: 941
gIndex: 368
gIndex: 450
gIndex: 85
gIndex: 482
gIndex: 326
gIndex: 621
gIndex: 354
gIndex: 818
gIndex: 811
gIndex: 48
gIndex: 360
gIndex: 1037
gIndex: 241
gIndex: 439
gIndex: 757
gIndex: 816
gIndex: 817
gIndex: 246
gIndex: 750
gIndex: 218
gIndex: 134
It took 0.005931 seconds (0.003393 CPU seconds) to calculate 30 genKinbVec().
Start iteration .....
d2eps: -1.3071e+02
d1eps: 2.7770
deps: 0.0212
iter: 0
m_eps: 0
0.9821
eps0: 0
0.9609
m_tolEps: 1e-10
d2eps: -1.2536e+02
d1eps: 0.0574
deps: 0.0005
iter: 1
m_eps: 0
0.9826
eps0: 0
0.9821
m_tolEps: 1e-10
d2eps: -1.2525e+02
d1eps: 2.5614e-05
deps: 2.0451e-07
iter: 2
m_eps: 0
0.9826
eps0: 0
0.9826
m_tolEps: 1e-10
d2eps: -1.2525e+02
d1eps: 5.0837e-12
deps: 4.0590e-14
iter: 3
m_eps: 0
0.9826
eps0: 0
0.9826
m_tolEps: 1e-10
UpdateEps iter: 3
eps:
0
0.9826
beta:
-37.5557
0.5975
0.3791
diffBeta: 0.00275036
Start updating tau...
iter: 0
beta:
-37.5557
0.5975
0.3791
tau: 0.0293943
d2eps: -1.2360e+02
d1eps: -2.2300
deps: -0.0180
iter: 0
m_eps: 0
0.9646
eps0: 0
0.9826
m_tolEps: 1e-10
d2eps: -1.2811e+02
d1eps: 0.0403
deps: 0.0003
iter: 1
m_eps: 0
0.9649
eps0: 0
0.9646
m_tolEps: 1e-10
d2eps: -1.2803e+02
d1eps: 1.2656e-05
deps: 9.8853e-08
iter: 2
m_eps: 0
0.9649
eps0: 0
0.9649
m_tolEps: 1e-10
d2eps: -1.2803e+02
d1eps: 1.2440e-12
deps: 9.7169e-15
iter: 3
m_eps: 0
0.9649
eps0: 0
0.9649
m_tolEps: 1e-10
UpdateEps iter: 3
eps:
0
0.9649
beta:
-37.5479
0.5974
0.3811
diffBeta: 0.00231347
Start updating tau...
iter: 1
beta:
-37.5479
0.5974
0.3811
tau: 0.0136161
It took 0.073767 seconds (0.073541 CPU seconds) to fit the null POLMM..
Start estimating variance ratio....
nSNPs for CV: 20
CV: 5.84339e-06
Complete the null model fitting in package GRAB: Complete Time: 2025-08-02 05:17:44.613291
>
> objPOLMMFile <- system.file("results", "objPOLMMFile.RData", package = "GRAB")
> save(obj.POLMM, file = objPOLMMFile)
Warning in gzfile(file, "wb") :
cannot open compressed file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/GRAB/results/objPOLMMFile.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: save -> gzfile
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.2
Check: installed package size
Result: NOTE
installed size is 17.7Mb
sub-directories of 1Mb or more:
extdata 2.1Mb
libs 14.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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