############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DOtools ### ############################################################################## ############################################################################## * checking for file ‘DOtools/DESCRIPTION’ ... OK * preparing ‘DOtools’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘DOtools.Rmd’ using rmarkdown oooo oooo . o8o . 888 888 .o8 `"' .o8 .ooooo. .ooooo. 888 888 .o888oo oooo ooo oo.ooooo. oooo .oooo.o .o888oo d88' "Y8 d88 88b 888 888 888 88. .8 888 88b 888 d88( "8 888 888 888ooo888 888 888 888 88..8 888 888 888 `"Y88b. 888 888 .o8 888 .o 888 888 888 . `888' 888 888 888 o. )88b 888 . Y8bod8P `Y8bod8P' o888o o888o "888" .8' 888bod8P' o888o 8""888P' "888" .o..P' 888 `Y8P' o888o @Teichmann lab ⚙️ Configuration: 🛠️ indata: /tmp/RtmpwmOSbv/file77ccf482dd8f/ad.h5ad 🛠️ model: Healthy_COVID19_PBMC.pkl 🛠️ transpose-input: False 🛠️ gene-file: None 🛠️ cell-file: None 🛠️ mode: best_match 🛠️ p-thres: 0.5 🛠️ majority-voting: True 🛠️ outdir: /tmp/RtmpwmOSbv/file77ccf482dd8f 🛠️ prefix: 🛠️ xlsx: False 🛠️ plot-results: False 🛠️ quiet: False 🛠️ over-clustering: leiden0.3 🛠️ min-prop: 0.0 📁 Input file is '/tmp/RtmpwmOSbv/file77ccf482dd8f/ad.h5ad' ⏳ Loading data ⚠️ Warning: invalid expression matrix, expect ALL genes and log1p normalized expression to 10000 counts per cell. The prediction result may not be accurate 🔬 Input data has 2807 cells and 800 genes 🔗 Matching reference genes in the model 🧬 609 features used for prediction ⚖️ Scaling input data 🖋️ Predicting labels ✅ Prediction done! 🗳️ Majority voting the predictions ✅ Majority voting done! [INFO] Your data doesn't have replicates! Artificial replicates will be simulated to run scanpro. [INFO] Simulation may take some minutes... [INFO] Generating 3 replicates and running 100 simulations... [INFO] Finished 100 simulations in 4.07 seconds oooo oooo . o8o . 888 888 .o8 `"' .o8 .ooooo. .ooooo. 888 888 .o888oo oooo ooo oo.ooooo. oooo .oooo.o .o888oo d88' "Y8 d88 88b 888 888 888 88. .8 888 88b 888 d88( "8 888 888 888ooo888 888 888 888 88..8 888 888 888 `"Y88b. 888 888 .o8 888 .o 888 888 888 . `888' 888 888 888 o. )88b 888 . Y8bod8P `Y8bod8P' o888o o888o "888" .8' 888bod8P' o888o 8""888P' "888" .o..P' 888 `Y8P' o888o @Teichmann lab ⚙️ Configuration: 🛠️ indata: /tmp/RtmpwmOSbv/file77ccf61dbb520/ad.h5ad 🛠️ model: Healthy_COVID19_PBMC.pkl 🛠️ transpose-input: False 🛠️ gene-file: None 🛠️ cell-file: None 🛠️ mode: best_match 🛠️ p-thres: 0.5 🛠️ majority-voting: True 🛠️ outdir: /tmp/RtmpwmOSbv/file77ccf61dbb520 🛠️ prefix: 🛠️ xlsx: False 🛠️ plot-results: False 🛠️ quiet: False 🛠️ over-clustering: annotation_recluster 🛠️ min-prop: 0.0 📁 Input file is '/tmp/RtmpwmOSbv/file77ccf61dbb520/ad.h5ad' ⏳ Loading data ⚠️ Warning: invalid expression matrix, expect ALL genes and log1p normalized expression to 10000 counts per cell. The prediction result may not be accurate 🔬 Input data has 1799 cells and 800 genes 🔗 Matching reference genes in the model 🧬 609 features used for prediction ⚖️ Scaling input data 🖋️ Predicting labels ✅ Prediction done! 🗳️ Majority voting the predictions ✅ Majority voting done! | | | 0% | |====== | 8% | |============ | 17% | |================== | 25% | |======================= | 33% | |============================= | 42% | |=================================== | 50% | |========================================= | 58% | |=============================================== | 67% | |==================================================== | 75% | |========================================================== | 83% | |================================================================ | 92% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Quitting from DOtools.Rmd:525-547 [GO analysis2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `curl::curl_fetch_memory()`: ! Timeout was reached [maayanlab.cloud]: Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds --- Backtrace: ▆ 1. └─DOtools::DO.enrichR(...) 2. └─enrichR::enrichr(genes = df_up[[gene_column]], databases = go_catgs) 3. └─enrichR:::getEnrichr(...) 4. └─base::tryCatch(...) 5. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 6. └─base (local) tryCatchOne(...) 7. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'DOtools.Rmd' failed with diagnostics: Timeout was reached [maayanlab.cloud]: Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds --- failed re-building ‘DOtools.Rmd’ SUMMARY: processing the following file failed: ‘DOtools.Rmd’ Error: Vignette re-building failed. Execution halted