After the update, no only disappeared some nodes, but all the R snippet in my previous works were resetted.
When i re execute them and i try to save them, at the subsequent start of knime i find all the node reset.
I think this is related to some changes in the behaviour of the nodes. I think it saves .Rdata not anymore in the workflow but in a temporary folder that is deleted when colosing knime.
Can you help? because i can’t use nothing of my work anymore since is all based on R snippet
@cosimotoma, sorry for the trouble. We’ll try to reproduce the R-problem immediately. Can you also provide more information which nodes disappeared after the update and what extensions you have installed?
Thanks!
Christian
I opened a topoc about this issue here Rest and excel nodes missing
i resolves uninstalling and reinstalling knime
for this specifi issue i can give you more information about the warnings i enocunter
Here are all the warnings that are in the log
WARN Math Formula 2:180:727:74 No configuration available
WARN SDF Writer 2:180:1505 Output file ‘C:\Users\CToma\Desktop\3d Azoles from tox21.sdf’ exists and must not be overwritten due to user settings
WARN Joiner 2:780:779:173 The bottom input table has changed. Some joining columns are missing: “CAS”
WARN Math Formula (Variable) 2:780:778:725 Unknown flow variable “${DMean}$$”
WARN Diversity Picker 2:780:776:831:892:883:885 Loading model settings failed: String for key “algorithm” not found.
WARN Diversity Picker 2:780:776:831:892:883:882 Loading model settings failed: String for key “algorithm” not found.
WARN Fingerprint Clustering 2:780:776:864:855 No column with a supported (SDF, MOL, MOL2, SMILES or CCT) molecule data type found
WARN Round Double 2:780:776:876:19:24 153 selected columns are not available anymore.
WARN Excel Writer (XLS) 2:780:776:876:19:25 Output file ‘C:\Users\CToma\Desktop\prova stratified vsurf.xlsx’ exists and will be overwritten
WARN Round Double 2:780:776:875:19:24 153 selected columns are not available anymore.
WARN Excel Writer (XLS) 2:780:776:875:19:25 Output file ‘C:\Users\CToma\Desktop\prova stratified vsurf.xlsx’ exists and will be overwritten
WARN Round Double 2:780:776:875:861:888 153 selected columns are not available anymore.
WARN Round Double 2:780:776:875:864:878 153 selected columns are not available anymore.
WARN Column Selection 2:780:776:853:0:0:891 Column ‘column1’ is not part of the table spec anymore.
Auto-guessing default column.
WARN Joiner 2:780:776:852:719:717 The top input table has changed. Some joining columns are missing: “First*(ID)”
WARN Joiner 2:780:776:852:845:717 The top input table has changed. Some joining columns are missing: “First*(ID)”
WARN Fingerprint Clustering 2:780:780:864:855 No column with a supported (SDF, MOL, MOL2, SMILES or CCT) molecule data type found
WARN CSV Writer 2:717:710:96:3 Output file ‘C:\Users\CToma\Desktop\conazoli.csv’ exists and must not be overwritten due to user settings
WARN CSV Writer 2:717:710:96:4 Output file ‘C:\Users\CToma\Desktop\conazolitest.csv’ exists and must not be overwritten due to user settings
WARN CSV Writer 2:717:710:811 Output file ‘C:\Users\CToma\Desktop\statistics best model Aromatase conazoles.csv’ exists and must not be overwritten due to user settings
WARN Table To Image 2:717:730:817 Found image column ‘Histogram’.
WARN CSV Writer 2:717:730:96:3 Output file ‘C:\Users\CToma\Desktop\conazoli.csv’ exists and must not be overwritten due to user settings
WARN CSV Writer 2:717:730:96:4 Output file ‘C:\Users\CToma\Desktop\conazolitest.csv’ exists and must not be overwritten due to user settings
WARN PCA Compute 2:717:730:96:800:768:7 column “nBM” not found, selected default columns
WARN GroupBy 2:717:730:96:800:768:769:58:49 No grouping column included. Aggregate complete table.
WARN SDF Writer 2:717:730:816 No structure column selected
WARN CSV Writer 2:717:730:811 Output file ‘C:\Users\CToma\Desktop\statistics best model Aromatase conazoles.csv’ exists and must not be overwritten due to user settings
WARN Histogram (interactive) 2:244:2 3 columns without a valid domain will be ignored. In order to calculate the domain use the Nominal Values or Domain Calculator node.
WARN CSV Writer 2:244:96:3 Output file ‘C:\Users\CToma\Desktop\conazoli.csv’ exists and must not be overwritten due to user settings
WARN CSV Writer 2:244:96:4 Output file ‘C:\Users\CToma\Desktop\conazolitest.csv’ exists and must not be overwritten due to user settings
WARN SVM Learner 2:244:76 Rejecting 1 column(s) due to incompatible type: [Set]
WARN Scorer 2:244:874:888 Column Cluster not found.
WARN SDF Writer 2:718:271 Structure column ‘SMILES normalizzate VEGA’ does not exist in input table
WARN Math Formula (Variable) 2:742:725 Unknown flow variable “${DMean}$$”
WARN CSV Writer 2:764 Output file ‘C:\Users\CToma\Desktop\Aromatasi\Solo conazoli per toropov\Conazoles for Toropov with inactives.csv’ exists and must not be overwritten due to user settings
WARN Molecule to CDK 2:766 No molecule column found
WARN Diversity Picker 2:748:864:862:741 Loading model settings failed: String for key “algorithm” not found.
WARN Round Double 2:748:875:19:24 53 selected columns are not available anymore.
WARN Excel Writer (XLS) 2:748:875:19:25 Output file ‘C:\Users\CToma\Desktop\prova stratified vsurf.xlsx’ exists and will be overwritten
WARN Round Double 2:748:875:861:888 53 selected columns are not available anymore.
WARN Round Double 2:748:875:864:878 53 selected columns are not available anymore.
WARN Naive Bayes Predictor 2:748:874:874:872 The following input columns are unknown and will be skipped: ID
WARN Naive Bayes Predictor 2:748:874:874:880 The following input columns are unknown and will be skipped: Set, ID, AC50
WARN Round Double 2:759:875:19:24 527 selected columns are not available anymore.
WARN Excel Writer (XLS) 2:759:875:19:25 Output file ‘C:\Users\CToma\Desktop\prova stratified vsurf.xlsx’ exists and will be overwritten
WARN Round Double 2:759:875:861:888 527 selected columns are not available anymore.
WARN Round Double 2:759:875:864:878 527 selected columns are not available anymore.
WARN Naive Bayes Predictor 2:759:874:874:872 The following input columns are unknown and will be skipped: ID
WARN Naive Bayes Predictor 2:759:874:874:880 The following input columns are unknown and will be skipped: Set, ID, AC50
WARN Column Selection 2:759:853:0:0:891 Column ‘column1’ is not part of the table spec anymore.
Auto-guessing default column.
WARN Round Double 2:759:853:880 17 selected columns are not available anymore.
WARN LoadWorkflowRunnable Warnings during load: Status: Warning: Aromatasi case weight prova miglioramento modello 2 loaded with warnings
WARN LoadWorkflowRunnable Status: Warning: Aromatasi case weight prova miglioramento modello 2
WARN LoadWorkflowRunnable Status: Warning: Prova workflow data curation 2:780
WARN LoadWorkflowRunnable Status: Warning: Antagonist modeling 2:780:776
WARN LoadWorkflowRunnable Status: Warning: Split and pre process 2:780:776:831
WARN LoadWorkflowRunnable Status: Warning: Conazole stratified splitting and clustering 2:780:776:831:892
WARN LoadWorkflowRunnable Status: Warning: split with conoszole treshold 2:780:776:831:892:883
WARN LoadWorkflowRunnable Status: Warning: Diversity Picker 2:780:776:831:892:883:885
WARN LoadWorkflowRunnable Status: Warning: Loading model settings failed: String for key “algorithm” not found.
WARN LoadWorkflowRunnable Status: Warning: Diversity Picker 2:780:776:831:892:883:882
WARN LoadWorkflowRunnable Status: Warning: Loading model settings failed: String for key “algorithm” not found.
WARN LoadWorkflowRunnable Status: Warning: Classification 2:780:780
WARN LoadWorkflowRunnable Status: Warning: Prova random forest unbalanced 2:780:780:875
WARN LoadWorkflowRunnable Status: Warning: VSURF feature selection 2:780:780:875:19
WARN LoadWorkflowRunnable Status: Warning: Some node states were invalid
WARN LoadWorkflowRunnable Status: Warning: Antagonist modeling 2:748
WARN LoadWorkflowRunnable Status: Warning: smiliar compunds 2:748:864
WARN LoadWorkflowRunnable Status: Warning: Split and pre process 2:748:864:862
WARN LoadWorkflowRunnable Status: Warning: Diversity Picker 2:748:864:862:741
WARN LoadWorkflowRunnable Status: Warning: Loading model settings failed: String for key “algorithm” not found.
Are also some nodes before the R-Snippet resettet or is it only the R-Snippet and subsequent nodes?
Yes that’s the strange thing. at first i thought this is was caused by the updare of LigandScout Extensions for the KNIME Workbench* provided by *Inte:Ligand GmbH, that require one addtional parameter for the algorithm. bur even when resetting all the nodes and trying to reexecute everything it keeps to reset
So, all nodes are resetted or just the R-Snippet nodes?
No, only R snippet nodes. If i take only the the branch with R spippets and delete everything it seems working. I imagine it’s related to a variable that messes with something in my nodes. The issue still remains, because if I open the old workflow it will reset, but at least i can continue to work.
Can you provide the log output and maybe even the knime.log file?