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jn-goe / gruffi

Granular Functional Filtering (Gruffi) to isolate stressed cells
GNU General Public License v3.0
11 stars 6 forks source link

Unable to load package #2

Closed wk-chan closed 2 years ago

wk-chan commented 2 years ago

Hello,

Firstly thank you for the tool. I've previously managed to run gruffi fine and it was helpful in better defining pseudotime for my dataset. However, recently I tried to run this again on another dataset but I was unable to load the package. Below is the error I'm getting:

Warning messages: 1: S3 method ‘plot.clust.size.distr’ was declared in NAMESPACE but not found 2: In setup_ns_exports(path, export_all, export_imports) : Objects listed as exports, but not present in namespace: AddCustomScore, AddGOGeneList.manual, AddGOScore, CalcTranscriptomePercentage, CalcTranscriptomePercentageGO, CleanDuplicateScorenames, CustomScoreEvaluation, FeaturePlotSaveCustomScore, FeaturePlotSaveGO, FilterStressedCells, GO_score_evaluation, GetAllGOTerms, GetGOTerms, GetNamedClusteringRuns, IntersectWithExpressed, PasteUniqueGeneList, PlotGoTermScores, PlotNormAndSkew, Shiny.GO.thresh, UMAP.3d.cubes, aut.res.clustering, calc.cluster.averages.gruffi, clUMAP.thresholding, fix.metad.Colname.rm.trailing.1, reassign.small.clusters, saveData, saveRDS.compress.in.BG, sparse.cor, stand_dev_skewed, ww.convert.GO_term.2.score, ww.convert.score.2.GO_term

vertesy commented 2 years ago

Hi,

so these are not errors, but warnings - meaning that the package was still loaded.

Please download the latest version. For me both of these commands work without any warning or error:

require(gruffi)
devtools::load_all(path = "~/GitHub/Packages/gruffi/")

Let me know if you still have the problem!

wk-chan commented 2 years ago

Thanks for getting back to me. I've removed the packages and tried to reinstall everything but now I've encountered this error while trying to install CodeAndRoll2:

Error: object ‘stopif’ is not exported by 'namespace:MarkdownReports' Execution halted

resulting in me unable to install gruffi.

vertesy commented 2 years ago

Hi,

could you try below and see if you still have the error:

devtools::install_github(repo = "vertesy/Stringendo", upgrade = F)
devtools::install_github(repo = "vertesy/ReadWriter", upgrade = F)
devtools::install_github(repo = "vertesy/CodeAndRoll2", upgrade = F)
devtools::install_github(repo = "vertesy/MarkdownHelpers", upgrade = F)
devtools::install_github(repo = "vertesy/MarkdownReports", upgrade = F)

Not sure why you got Error: object ‘stopif’ is not exported by 'namespace:MarkdownReports', but I removed one part that may have caused it.

wk-chan commented 2 years ago

Hi, I've tried the following and I'm still having the error.

I'm not sure what is causing it.

vertesy commented 2 years ago

Hi, sorry for the late follow up! I now successfully installed it on three new computers, and updated some the dependencies, so I believe if you use the latest versions, you should be fine. Sorry for your troubles with getting it to run.