Error(s) in re-building vignettes:
  ...
--- re-building ‘GEO_App.Rmd’ using rmarkdown
trying URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178620&format=file&file=GSE178620%5Fraw%5Fabundances%2Ecsv%2Egz'
Content type 'application/octet-stream' length 1892945 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bulkAnalyseR.Rcheck/vign_test/bulkAnalyseR/vignettes/GEO_App_files/figure-html/preprocess-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31284 bytes
Input file size = 31398 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 27518
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 27518

Output IDAT size = 27518 bytes (3766 bytes decrease)
Output file size = 27596 bytes (3802 bytes = 12.11% decrease)

[WARNING] Div at GEO_App.knit.md line 10 column 1 unclosed at GEO_App.knit.md line 200 column 1, closing implicitly.
--- finished re-building ‘GEO_App.Rmd’

--- re-building ‘IntegratingMultiomics.Rmd’ using rmarkdown

Quitting from IntegratingMultiomics.Rmd:155-168 [li data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://raw.githubusercontent.com/Core-Bioinformatics/bulkAnalyseR/master/exampledata/Li2021_miRNA_mRNA/expression_matrix_mRNA_preprocessed.csv'
---
Backtrace:
    ▆
 1. ├─... %>% as.matrix
 2. ├─base::as.matrix(.)
 3. └─utils::read.csv(...)
 4.   └─utils::read.table(...)
 5.     ├─base::open(file, "rt")
 6.     └─base::open.connection(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'IntegratingMultiomics.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/Core-Bioinformatics/bulkAnalyseR/master/exampledata/Li2021_miRNA_mRNA/expression_matrix_mRNA_preprocessed.csv'
--- failed re-building ‘IntegratingMultiomics.Rmd’

--- re-building ‘bulkAnalyseR.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bulkAnalyseR.Rcheck/vign_test/bulkAnalyseR/vignettes/bulkAnalyseR_files/figure-html/preprocess-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56447 bytes
Input file size = 56597 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 48532
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 48532

Output IDAT size = 48532 bytes (7915 bytes decrease)
Output file size = 48610 bytes (7987 bytes = 14.11% decrease)

[WARNING] Div at bulkAnalyseR.knit.md line 10 column 1 unclosed at bulkAnalyseR.knit.md line 603 column 1, closing implicitly.
--- finished re-building ‘bulkAnalyseR.Rmd’

SUMMARY: processing the following file failed:
  ‘IntegratingMultiomics.Rmd’

Error: Vignette re-building failed.
Execution halted