Package suggested but not available for checking: ‘dittoSeq’
Error(s) in re-building vignettes:
--- re-building ‘Download.Rmd’ using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
Quitting from lines 421-429 (Download.Rmd) 
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'dittoSeq'
--- failed re-building ‘Download.Rmd’

--- re-building ‘Upload.Rmd’ using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
ejecting cassette: Upload-vignette
CrulAdapter disabled!
HttrAdapter disabled!
net connect disabled
--- finished re-building ‘Upload.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘dittoSeq’
Error(s) in re-building vignettes:
--- re-building ‘Download.Rmd’ using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
Quitting from lines 421-429 (Download.Rmd) 
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'dittoSeq'
--- failed re-building ‘Download.Rmd’

--- re-building ‘Upload.Rmd’ using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
ejecting cassette: Upload-vignette
CrulAdapter disabled!
HttrAdapter disabled!
net connect disabled
--- finished re-building ‘Upload.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'dittoSeq'
Error(s) in re-building vignettes:
  ...
--- re-building 'Download.Rmd' using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
Quitting from lines 421-429 (Download.Rmd) 
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'dittoSeq'
--- failed re-building 'Download.Rmd'

--- re-building 'Upload.Rmd' using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
ejecting cassette: Upload-vignette
CrulAdapter disabled!
HttrAdapter disabled!
net connect disabled
--- finished re-building 'Upload.Rmd'

SUMMARY: processing the following file failed:
  'Download.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘dittoSeq’
Error(s) in re-building vignettes:
--- re-building ‘Download.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Bioconductor version '3.11' is out-of-date; the current release version '3.12'
  is available with R version '4.0'; see https://bioconductor.org/install
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
Quitting from lines 421-429 (Download.Rmd) 
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'dittoSeq'
--- failed re-building ‘Download.Rmd’

--- re-building ‘Upload.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Bioconductor version '3.11' is out-of-date; the current release version '3.12'
  is available with R version '4.0'; see https://bioconductor.org/install
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
ejecting cassette: Upload-vignette
CrulAdapter disabled!
HttrAdapter disabled!
net connect disabled
--- finished re-building ‘Upload.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'dittoSeq', 'BiocStyle'
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: subscript out of bounds
  Backtrace:
      █
   1. ├─vcr::use_cassette(...) test-update.R:10:0
   2. │ └─cassette$call_block(...)
   3. └─magmaR::retrieveMatrix(targ, "example", "rna_seq", "all", "gene_counts") test-update.R:11:4
   4.   └─base::lapply(...)
   5.     └─magmaR:::FUN(X[[i]], ...)
   6.       └─magmaR:::.matrix_retrieval_chunk(...)
   7.         └─base::lapply(...)
   8.           └─magmaR:::FUN(X[[i]], ...)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Download.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 18-31 (Download.Rmd) 
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘Download.Rmd’

--- re-building ‘Upload.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 18-31 (Upload.Rmd) 
Error: processing vignette 'Upload.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘Upload.Rmd’

SUMMARY: processing the following files failed:
  ‘Download.Rmd’ ‘Upload.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'dittoSeq'
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > test_check("magmaR")
  Loading required package: magmaR
  == Failed tests ================================================================
  -- Error (test-matrix.R:14:9): retrieveMatrix ----------------------------------
  Error: subscript out of bounds
  Backtrace:
      x
   1. \-magmaR::retrieveMatrix(targ, "example", "rna_seq", attributeNames = "gene_counts") test-matrix.R:14:8
   2.   \-base::lapply(...)
   3.     \-magmaR:::FUN(X[[i]], ...)
   4.       \-magmaR:::.matrix_retrieval_chunk(...)
   5.         \-base::lapply(...)
   6.           \-magmaR:::FUN(X[[i]], ...)
  -- Failure (test-matrix.R:41:9): retrieveMatrix warns but ignores empty records --
  `mat` has type 'logical', not 'integer'.
  -- Failure (test-matrix.R:42:9): retrieveMatrix warns but ignores empty records --
  dim(mat) not equal to c(40, 12).
  2/2 mismatches (average diff: 26)
  [1] 0 - 40 == -40
  [2] 0 - 12 == -12
  -- Failure (test-special.R:26:3): retrieveIds ----------------------------------
  `ret` has type 'integer', not 'character'.
  -- Error (test-update.R:10:1): (code run outside of `test_that()`) -------------
  Error: subscript out of bounds
  Backtrace:
      x
   1. +-vcr::use_cassette(...) test-update.R:10:0
   2. | \-cassette$call_block(...)
   3. \-magmaR::retrieveMatrix(targ, "example", "rna_seq", "all", "gene_counts") test-update.R:11:4
   4.   \-base::lapply(...)
   5.     \-magmaR:::FUN(X[[i]], ...)
   6.       \-magmaR:::.matrix_retrieval_chunk(...)
   7.         \-base::lapply(...)
   8.           \-magmaR:::FUN(X[[i]], ...)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Download.Rmd' using rmarkdown
Bioconductor version '3.10' is out-of-date; the current release version '3.12'
  is available with R version '4.0'; see https://bioconductor.org/install
Quitting from lines 18-31 (Download.Rmd) 
Error: processing vignette 'Download.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'Download.Rmd'

--- re-building 'Upload.Rmd' using rmarkdown
Bioconductor version '3.10' is out-of-date; the current release version '3.12'
  is available with R version '4.0'; see https://bioconductor.org/install
Quitting from lines 18-31 (Upload.Rmd) 
Error: processing vignette 'Upload.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'Upload.Rmd'

SUMMARY: processing the following files failed:
  'Download.Rmd' 'Upload.Rmd'

Error: Vignette re-building failed.
Execution halted