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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RNAmodR
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* checking for file ‘RNAmodR/DESCRIPTION’ ... OK
* preparing ‘RNAmodR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RNAmodR.Rmd’ using rmarkdown
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add478e976e_2541'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add4d7d65df_2537'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add2ae910d4_2543'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add6302dbbe_2545'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add7ebccaff_2539'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add7953fbb4_2547'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add77844c31_2549'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add478e976e_2541'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add4d7d65df_2537'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add6302dbbe_2545'

Quitting from RNAmodR.Rmd:254-256 [modifierset1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `reducer$value.cache[[as.character(idx)]] <- values`:
! wrong args for environment subassignment
---
Backtrace:
     ▆
  1. └─RNAmodR::ModSetInosine(files, annotation = annotation, sequences = sequences)
  2.   ├─RNAmodR::ModifierSet(...)
  3.   └─RNAmodR::ModifierSet(...)
  4.     └─RNAmodR:::.bamfiles_to_ModifierSet(...)
  5.       ├─BiocParallel::bpmapply(...)
  6.       └─BiocParallel::bpmapply(...)
  7.         ├─BiocParallel::bpmapply(...)
  8.         └─BiocParallel::bpmapply(...)
  9.           ├─BiocParallel::bplapply(...)
 10.           └─BiocParallel::bplapply(...)
 11.             └─BiocParallel:::.bpinit(...)
 12.               ├─BiocParallel::bploop(...)
 13.               └─BiocParallel:::bploop.lapply(...)
 14.                 └─BiocParallel:::.bploop_impl(...)
 15.                   └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
 16.                     ├─BiocParallel:::.reducer_add(reducer, njob, value)
 17.                     └─BiocParallel:::.reducer_add(reducer, njob, value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RNAmodR.Rmd' failed with diagnostics:
wrong args for environment subassignment
--- failed re-building ‘RNAmodR.Rmd’

--- re-building ‘RNAmodR.creation.Rmd’ using rmarkdown
Warning in dir.create(biocDir) :
  cannot create dir '/tmp/RtmpaXLKFO/BiocStyle', reason 'No such file or directory'
Warning in file(con, "w") :
  cannot open file '/tmp/RtmpaXLKFO/BiocStyle/template.html': No such file or directory
Error: processing vignette 'RNAmodR.creation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘RNAmodR.creation.Rmd’

SUMMARY: processing the following files failed:
  ‘RNAmodR.Rmd’ ‘RNAmodR.creation.Rmd’

Error: Vignette re-building failed.
Execution halted