Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/imageTCGAutils
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 24.04.3 LTS)/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo1 Summary

[top]

Package: imageTCGAutils
Version: 0.99.20
RVersion: 4.6
BiocVersion: 3.23
BuildCommand: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data imageTCGAutils
BuildTime: 1 minutes 0.36 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: imageTCGAutils_20260319170418
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: imageTCGAutils. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

nebbiolo1 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘imageTCGAutils/DESCRIPTION’ ... OK
* preparing ‘imageTCGAutils’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘imageTCGAutils.Rmd’ using rmarkdown

Download status: 0 done; 1 in progress (0 b/s). Total size: 4.00 Kb (0%)...
Download status: 0 done; 1 in progress (928.94 Kb/s). Total size: 5.12 Mb (17%)...
Download status: 0 done; 1 in progress (1.09 Mb/s). Total size: 11.53 Mb (38%)...
Download status: 0 done; 1 in progress (1.15 Mb/s). Total size: 18.08 Mb (59%)...
Download status: 0 done; 1 in progress (1.18 Mb/s). Total size: 24.65 Mb (81%)...
Download status: 1 done; 0 in progress. Total size: 30.60 Mb (100%)... done!             

Quitting from imageTCGAutils.Rmd:85-99 [import tile-level emb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `BiocFileCache::bfcadd()`:
! all(rtype == "web" | file.exists(fpath)) is not TRUE
---
Backtrace:
     ▆
  1. ├─dplyr::pull(...)
  2. ├─dplyr::filter(getCatalog("provgigapath"), Project.ID == "TCGA-OV")
  3. └─imageFeatureTCGA::getCatalog("provgigapath")
  4.   ├─readr::read_tsv(.download_catalog(redownload = redownload), col_types = .CATALOG_COL_TYPES)
  5.   │ └─readr:::standardise_literal_data(...)
  6.   └─imageFeatureTCGA:::.download_catalog(redownload = redownload)
  7.     └─imageFeatureTCGA:::.cache_url_files(...)
  8.       └─base::mapply(...)
  9.         └─imageFeatureTCGA (local) `<fn>`(...)
 10.           ├─BiocFileCache::bfcadd(...)
 11.           └─BiocFileCache::bfcadd(...)
 12.             └─base::stopifnot(all(rtype == "web" | file.exists(fpath)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'imageTCGAutils.Rmd' failed with diagnostics:
all(rtype == "web" | file.exists(fpath)) is not TRUE
--- failed re-building ‘imageTCGAutils.Rmd’

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

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

[top]


                				
 

                            
 
                                
                				
nebbiolo1 BUILD BIN output
 
                    			
[top]