Last updated on 2026-10-24 15:51:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.6 | 27.12 | 271.12 | 298.24 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.6 | 19.08 | 170.65 | 189.73 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.6 | 23.00 | 212.72 | 235.72 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.6 | 19.00 | 181.04 | 200.04 | OK | |
| r-devel-windows-x86_64 | 1.1.6 | 32.00 | 290.00 | 322.00 | OK | |
| r-patched-linux-x86_64 | 1.1.6 | 27.13 | 262.68 | 289.81 | OK | |
| r-release-linux-x86_64 | 1.1.6 | 27.74 | 261.96 | 289.70 | OK | |
| r-release-macos-arm64 | 1.1.6 | 7.00 | 99.00 | 106.00 | OK | |
| r-release-macos-x86_64 | 1.1.6 | 20.00 | 207.00 | 227.00 | OK | |
| r-release-windows-x86_64 | 1.1.6 | 30.00 | 264.00 | 294.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.6 | 2.00 | 5.00 | 7.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.6 | 19.00 | 196.00 | 215.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.6 | 43.00 | 351.00 | 394.00 | OK |
Version: 1.1.6
Check: examples
Result: ERROR
Running examples in ‘plasma-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SingleModel-class
> ### Title: Class '"SingleModel"'
> ### Aliases: fitSingleModel SingleModel-class predict,SingleModel-method
> ### summary,SingleModel-method plot,SingleModel,missing-method
> ### fitSingleModel
> ### Keywords: classes
>
> ### ** Examples
>
> fls <- try(loadESCAdata())
> if (inherits(fls, "try-error")) {
+ stop("Unable to load data from remote server.")
+ }
> MO <- with(plasmaEnv, prepareMultiOmics(assemble, Outcome) )
> MO <- MO[c("ClinicalBin", "ClinicalCont", "RPPA"),]
> set.seed(98765)
> splitVec <- with(plasmaEnv, rbinom(nrow(Outcome), 1, 0.6))
> trainD <- MO[, splitVec == 1]
> testD <- MO[, splitVec == 0]
>
> zerothPass <- fitSingleModel(trainD, N = "RPPA",
+ timevar = "Days", eventvar = "vital_status",
+ eventvalue = "dead")
____************************************************____
Error in a$specials[[i]] : subscript out of bounds
Calls: fitSingleModel ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.6
Check: tests
Result: ERROR
Running ‘test01-MO.R’ [9s/13s]
Running ‘test02-fitCox.R’ [7s/11s]
Running ‘test03-multiplePLS.R’ [7s/11s]
Running ‘test04-plasma.R’ [7s/11s]
Running ‘test05-interpret.R’ [8s/11s]
Running the tests in ‘tests/test02-fitCox.R’ failed.
Complete output:
> library(plasma)
> # Repeat basic stuff from first test
> fls <- try(loadESCAdata())
> if (inherits(fls, "try-error")) {
+ stop("Unable to load data from remote server.")
+ }
> ls()
[1] "fls"
> MO <- with(plasmaEnv, prepareMultiOmics(assemble, Outcome))
> train <- rep(c(TRUE, FALSE), times = c(112, 185-112))
> MO2 <- MO[, train]
> ## Fit a survival model on a single data set on the MultiOmics object
> fitted <- fitSingleModel(MO2, "ClinicalBin", "Days", "vital_status", "dead")
____************************************************____
____There are some NAs in X but not in Y____
Error in a$specials[[i]] : subscript out of bounds
Calls: fitSingleModel ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Running the tests in ‘tests/test03-multiplePLS.R’ failed.
Complete output:
> library(plasma)
> fls <- try(loadESCAdata())
> if (inherits(fls, "try-error")) {
+ stop("Unable to load data from remote server.")
+ }
> ls()
[1] "fls"
> ## prepare MultiOmics
> MO <- with(plasmaEnv, prepareMultiOmics(assemble, Outcome))
> MO <- MO[c("ClinicalBin", "ClinicalCont", "RPPA"),]
> summary(MO)
Datasets:
ClinicalBin ClinicalCont RPPA
[1,] 53 6 192
[2,] 185 185 185
Outcomes:
patient_id vital_status days_to_death days_to_last_followup
a3i8 : 1 alive:108 Min. : 9.0 Min. : 4.0
a3ql : 1 dead : 77 1st Qu.: 180.0 1st Qu.: 336.5
a3y9 : 1 Median : 351.0 Median : 402.5
a3ya : 1 Mean : 495.2 Mean : 570.1
a3yb : 1 3rd Qu.: 650.0 3rd Qu.: 696.8
a3yc : 1 Max. :2532.0 Max. :3714.0
(Other):179 NAs :108 NAs :77
Days
Min. : 4.0
1st Qu.: 232.0
Median : 400.0
Mean : 538.9
3rd Qu.: 681.0
Max. :3714.0
> ## test complete cox models
> set.seed(12345)
> train <- rep(FALSE, 185)
> train[sample(185, 113)] <- TRUE
> MO2 <- MO[, train]
> summary(MO2)
Datasets:
ClinicalBin ClinicalCont RPPA
[1,] 53 6 192
[2,] 113 113 113
Outcomes:
patient_id vital_status days_to_death days_to_last_followup
a3ql : 1 alive:64 Min. : 9.0 Min. : 11.0
a3y9 : 1 dead :49 1st Qu.: 157.0 1st Qu.: 318.8
a3ya : 1 Median : 351.0 Median : 404.5
a3yc : 1 Mean : 494.6 Mean : 572.7
a43c : 1 3rd Qu.: 600.0 3rd Qu.: 652.8
a43h : 1 Max. :2532.0 Max. :3714.0
(Other):107 NAs :64 NAs :49
Days
Min. : 9.0
1st Qu.: 238.0
Median : 400.0
Mean : 538.8
3rd Qu.: 632.0
Max. :3714.0
> bigfit <- fitCoxModels(MO2, timevar = "Days",
+ eventvar = "vital_status",
+ eventvalue = "dead")
Fitting model with ClinicalBin
____************************************************____
____There are some NAs in X but not in Y____
Error in a$specials[[i]] : subscript out of bounds
Calls: fitCoxModels ... model.matrix -> model.matrix.coxph -> delete.response -> off
In addition: Warning message:
In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; coefficient may be infinite.
Execution halted
Running the tests in ‘tests/test04-plasma.R’ failed.
Complete output:
> library(plasma)
> fls <- try(loadESCAdata())
> if (inherits(fls, "try-error")) {
+ stop("Unable to load data from remote server.")
+ }
> ls()
[1] "fls"
> ## prepare MultiOmics
> MO <- with(plasmaEnv, prepareMultiOmics(assemble, Outcome))
> MO <- MO[c("ClinicalBin", "ClinicalCont", "RPPA"),]
> summary(MO)
Datasets:
ClinicalBin ClinicalCont RPPA
[1,] 53 6 192
[2,] 185 185 185
Outcomes:
patient_id vital_status days_to_death days_to_last_followup
a3i8 : 1 alive:108 Min. : 9.0 Min. : 4.0
a3ql : 1 dead : 77 1st Qu.: 180.0 1st Qu.: 336.5
a3y9 : 1 Median : 351.0 Median : 402.5
a3ya : 1 Mean : 495.2 Mean : 570.1
a3yb : 1 3rd Qu.: 650.0 3rd Qu.: 696.8
a3yc : 1 Max. :2532.0 Max. :3714.0
(Other):179 NAs :108 NAs :77
Days
Min. : 4.0
1st Qu.: 232.0
Median : 400.0
Mean : 538.9
3rd Qu.: 681.0
Max. :3714.0
> ## split into train and test
> set.seed(12345)
> train <- rep(FALSE, 185)
> train[sample(185, 113)] <- TRUE
> MO2 <- MO[, train]
> summary(MO2)
Datasets:
ClinicalBin ClinicalCont RPPA
[1,] 53 6 192
[2,] 113 113 113
Outcomes:
patient_id vital_status days_to_death days_to_last_followup
a3ql : 1 alive:64 Min. : 9.0 Min. : 11.0
a3y9 : 1 dead :49 1st Qu.: 157.0 1st Qu.: 318.8
a3ya : 1 Median : 351.0 Median : 404.5
a3yc : 1 Mean : 494.6 Mean : 572.7
a43c : 1 3rd Qu.: 600.0 3rd Qu.: 652.8
a43h : 1 Max. :2532.0 Max. :3714.0
(Other):107 NAs :64 NAs :49
Days
Min. : 9.0
1st Qu.: 238.0
Median : 400.0
Mean : 538.8
3rd Qu.: 632.0
Max. :3714.0
> ## test complete cox models
> bigfit <- fitCoxModels(MO2, "Days", "vital_status", "dead")
Fitting model with ClinicalBin
____************************************************____
____There are some NAs in X but not in Y____
Error in a$specials[[i]] : subscript out of bounds
Calls: fitCoxModels ... model.matrix -> model.matrix.coxph -> delete.response -> off
In addition: Warning message:
In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; coefficient may be infinite.
Execution halted
Running the tests in ‘tests/test05-interpret.R’ failed.
Complete output:
> library(plasma)
> fls <- try(loadESCAdata())
> if (inherits(fls, "try-error")) {
+ stop("Unable to load data from remote server.")
+ }
> ls()
[1] "fls"
> ## prepare MultiOmics
> MO <- with(plasmaEnv, prepareMultiOmics(assemble, Outcome) )
> MO <- MO[c("ClinicalBin", "ClinicalCont", "RPPA"),]
> summary(MO)
Datasets:
ClinicalBin ClinicalCont RPPA
[1,] 53 6 192
[2,] 185 185 185
Outcomes:
patient_id vital_status days_to_death days_to_last_followup
a3i8 : 1 alive:108 Min. : 9.0 Min. : 4.0
a3ql : 1 dead : 77 1st Qu.: 180.0 1st Qu.: 336.5
a3y9 : 1 Median : 351.0 Median : 402.5
a3ya : 1 Mean : 495.2 Mean : 570.1
a3yb : 1 3rd Qu.: 650.0 3rd Qu.: 696.8
a3yc : 1 Max. :2532.0 Max. :3714.0
(Other):179 NAs :108 NAs :77
Days
Min. : 4.0
1st Qu.: 232.0
Median : 400.0
Mean : 538.9
3rd Qu.: 681.0
Max. :3714.0
> ## split into train and test
> set.seed(12345)
> train <- rep(FALSE, 185)
> train[sample(185, 113)] <- TRUE
> MO2 <- MO[, train]
> summary(MO2)
Datasets:
ClinicalBin ClinicalCont RPPA
[1,] 53 6 192
[2,] 113 113 113
Outcomes:
patient_id vital_status days_to_death days_to_last_followup
a3ql : 1 alive:64 Min. : 9.0 Min. : 11.0
a3y9 : 1 dead :49 1st Qu.: 157.0 1st Qu.: 318.8
a3ya : 1 Median : 351.0 Median : 404.5
a3yc : 1 Mean : 494.6 Mean : 572.7
a43c : 1 3rd Qu.: 600.0 3rd Qu.: 652.8
a43h : 1 Max. :2532.0 Max. :3714.0
(Other):107 NAs :64 NAs :49
Days
Min. : 9.0
1st Qu.: 238.0
Median : 400.0
Mean : 538.8
3rd Qu.: 632.0
Max. :3714.0
> ## test complete cox models
> bigfit <- fitCoxModels(MO2, "Days", "vital_status", "dead")
Fitting model with ClinicalBin
____************************************************____
____There are some NAs in X but not in Y____
Error in a$specials[[i]] : subscript out of bounds
Calls: fitCoxModels ... model.matrix -> model.matrix.coxph -> delete.response -> off
In addition: Warning message:
In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; coefficient may be infinite.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.6
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-macos-arm64