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###
### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TPP
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* checking for file ‘TPP/DESCRIPTION’ ... OK
* preparing ‘TPP’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘NPARC_analysis_of_TPP_TR_data.Rnw’ using knitr
--- finished re-building ‘NPARC_analysis_of_TPP_TR_data.Rnw’

--- re-building ‘TPP_introduction_1D.Rnw’ using knitr

Quitting from TPP_introduction_1D.Rnw:409-415 [analyzeCCR]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `purrr::map()`:
i In index: 1.
i With name: Panobinostat_1.
Caused by error:
! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct.
i Please use `tibble::as_tibble()` instead.
---
Backtrace:
     x
  1. +-TPP::analyzeTPPCCR(...)
  2. | \-TPP::tppccrCurveFit(...)
  3. |   \-TPP:::eSetsToLongTable_fc(data)
  4. |     \-... %>% select(-colName, colName = colNameOrig)
  5. +-dplyr::select(., -colName, colName = colNameOrig)
  6. +-dplyr::left_join(., expInfo, by = c("experiment", "colName"))
  7. +-dplyr::mutate_if(., is.character, factor)
  8. | \-dplyr:::check_grouped(.tbl, "mutate", "if")
  9. |   \-dplyr::is_grouped_df(tbl)
 10. +-dplyr::rename(., id = gene, foldChange = value, colName = sample)
 11. +-dplyr::bind_rows(., .id = "experiment")
 12. | \-rlang::list2(...)
 13. \-purrr::map(., biobroom::tidy.ExpressionSet)
 14.   \-purrr:::map_("list", .x, .f, ..., .progress = .progress)
 15.     +-purrr:::with_indexed_errors(...)
 16.     | \-base::withCallingHandlers(...)
 17.     +-purrr:::call_with_cleanup(...)
 18.     \-biobroom (local) .f(.x[[i]], ...)
 19.       \-biobroom:::finish(ret)
 20.         \-dplyr::tbl_df(x)
 21.           \-lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()")
 22.             \-lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'TPP_introduction_1D.Rnw' failed with diagnostics:
ℹ In index: 1.
ℹ With name: Panobinostat_1.
Caused by error:
! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct.
ℹ Please use `tibble::as_tibble()` instead.
--- failed re-building ‘TPP_introduction_1D.Rnw’

--- re-building ‘TPP_introduction_2D.Rnw’ using knitr

Quitting from TPP_introduction_2D.Rnw:150-162 [ttp2dworkflow]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `purrr::map()`:
i In index: 1.
i With name: Panobinostat.
Caused by error:
! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct.
i Please use `tibble::as_tibble()` instead.
---
Backtrace:
     x
  1. +-TPP::analyze2DTPP(...)
  2. | \-TPP::tpp2dCurveFit(...)
  3. |   +-base::suppressWarnings(...)
  4. |   | \-base::withCallingHandlers(...)
  5. |   \-TPP::analyzeTPPCCR(...)
  6. |     \-TPP::tppccrCurveFit(...)
  7. |       \-TPP:::eSetsToLongTable_fc(data)
  8. |         \-... %>% select(-colName, colName = colNameOrig)
  9. +-dplyr::select(., -colName, colName = colNameOrig)
 10. +-dplyr::left_join(., expInfo, by = c("experiment", "colName"))
 11. +-dplyr::mutate_if(., is.character, factor)
 12. | \-dplyr:::check_grouped(.tbl, "mutate", "if")
 13. |   \-dplyr::is_grouped_df(tbl)
 14. +-dplyr::rename(., id = gene, foldChange = value, colName = sample)
 15. +-dplyr::bind_rows(., .id = "experiment")
 16. | \-rlang::list2(...)
 17. \-purrr::map(., biobroom::tidy.ExpressionSet)
 18.   \-purrr:::map_("list", .x, .f, ..., .progress = .progress)
 19.     +-purrr:::with_indexed_errors(...)
 20.     | \-base::withCallingHandlers(...)
 21.     +-purrr:::call_with_cleanup(...)
 22.     \-biobroom (local) .f(.x[[i]], ...)
 23.       \-biobroom:::finish(ret)
 24.         \-dplyr::tbl_df(x)
 25.           \-lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()")
 26.             \-lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'TPP_introduction_2D.Rnw' failed with diagnostics:
ℹ In index: 1.
ℹ With name: Panobinostat.
Caused by error:
! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct.
ℹ Please use `tibble::as_tibble()` instead.
--- failed re-building ‘TPP_introduction_2D.Rnw’

SUMMARY: processing the following files failed:
  ‘TPP_introduction_1D.Rnw’ ‘TPP_introduction_2D.Rnw’

Error: Vignette re-building failed.
Execution halted