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==========================================================================
  IOBR v0.99.99  Immuno-Oncology Biological Research 
  For Tutorial: https://iobr.github.io/book/
  For Help: https://github.com/IOBR/IOBR/issues

 If you use IOBR in published research, please cite:
 DQ Zeng, YR Fang, ..., GC Yu*, WJ Liao*, 
 Enhancing immuno-oncology investigations through multidimensional decoding 
 of tumor microenvironment with IOBR 2.0. Cell Rep Methods 4, 100910 (2024). 
 &  
 YR Fang, ..., WJ Liao*, DQ Zeng*, 
 Systematic Investigation of Tumor Microenvironment and 
 Antitumor Immunity With IOBR, Med Research (2025). 
 https://onlinelibrary.wiley.com/doi/epdf/10.1002/mdr2.70001 
==========================================================================

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Listening on http://127.0.0.1:35323
Warning in .load_data("anno_grch38") :
  sysdata.rda not found in IOBR package
>>>--- Using variables (anno_grch38) and gene lengths (eff_length)  built into the IOBR package to perform TPM transformation
>>>--- The gene lengths (eff_length) was estimated by function `getGeneLengthAndGCContent` from EDASeq package with default parameters at 2023-02-10
Warning in count2tpm(countMat = data, idType = input$count2tpm_idType, org = input$count2tpm_org,  :
  >>>--- Omit 3985 genes of which length is not available !
>>> log2 transformation was finished
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/find_outlier_samples_project', reason 'Permission denied'
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/find_outlier_samples_project', reason 'Permission denied'

>>> Calculating signature score using ssGSEA method
>>> log2 transformation is not necessary

>>> Running EPIC
Warning in IOBR::EPIC(bulk = eset, reference = ref, mRNA_cell = NULL, scaleExprs = TRUE) :
  The optimization didn't fully converge for some samples:
TCGA-BR-A4J4
 - check fit.gof for the convergeCode and convergeMessage
Warning in IOBR::EPIC(bulk = eset, reference = ref, mRNA_cell = NULL, scaleExprs = TRUE) :
  mRNA_cell value unknown for some cell types: CAFs, Endothelial - using the default value of 0.4 for these but this might bias the true cell proportions from all cell types.


Closed TCGA pool.
Closed OtherCohort pool.
Closed immunotherapy pool.
Closed cancercohort pool.
Execution halted