Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
> 
> ### ** Examples
> 
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done

ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done

> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done

ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done

> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+     # Only running a few iterations for fast examples
+     pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+     pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
calcAgreement 9.526  1.466   8.859
createLiger   6.145  0.197   8.617
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
> 
> ### ** Examples
> 
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done

ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done

> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done

ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done

> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+     # Only running a few iterations for fast examples
+     pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+     pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
calcAgreement 5.388  2.878  11.712
Running examples in 'rliger-Ex.R' failed
The error most likely occurred in:

> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
> 
> ### ** Examples
> 
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done

ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done

> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done

ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done

> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+     # Only running a few iterations for fast examples
+     pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+     pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
> 
> ### ** Examples
> 
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done

ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done

> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done

ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done

> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+     # Only running a few iterations for fast examples
+     pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+     pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
createLiger   5.510  0.221   6.130
calcAgreement 4.725  1.003   8.165
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
> 
> ### ** Examples
> 
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done

ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done

> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done

ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done

> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+     # Only running a few iterations for fast examples
+     pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+     pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
createLiger   5.659  0.197   7.074
calcAgreement 4.726  1.103   8.372
Running examples in 'rliger-Ex.R' failed
The error most likely occurred in:

> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
> 
> ### ** Examples
> 
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done

ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done

> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done

ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done

> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+     # Only running a few iterations for fast examples
+     pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+     pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Packages suggested but not available for checking:
  'DoubletFinder', 'RcppPlanc', 'reactome.db'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   6.4Mb
Packages suggested but not available for checking:
  'DoubletFinder', 'RcppPlanc'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   6.2Mb
Package suggested but not available for checking: 'DoubletFinder'
Running examples in 'rliger-Ex.R' failed
The error most likely occurred in:

> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
> 
> ### ** Examples
> 
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done

ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done

> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done

ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done

> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+     # Only running a few iterations for fast examples
+     pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+     pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted