############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fobitools ### ############################################################################## ############################################################################## * checking for file ‘fobitools/DESCRIPTION’ ... OK * preparing ‘fobitools’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Dietary_data_annotation.Rmd’ using rmarkdown Registered S3 methods overwritten by 'readr': method from as.data.frame.spec_tbl_df vroom as_tibble.spec_tbl_df vroom format.col_spec vroom print.col_spec vroom print.collector vroom print.date_names vroom print.locale vroom str.col_spec vroom ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ✔ ggplot2 3.3.6 ✔ purrr 0.3.4 ✔ tibble 3.1.7 ✔ dplyr 1.0.9 ✔ tidyr 1.2.0 ✔ stringr 1.4.0 ✔ readr 2.1.2 ✔ forcats 0.5.1 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Attaching package: 'kableExtra' The following object is masked from 'package:dplyr': group_rows Warning: ggrepel: 122 unlabeled data points (too many overlaps). Consider increasing max.overlaps Warning: ggrepel: 122 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘Dietary_data_annotation.Rmd’ --- re-building ‘MW_ST000291_enrichment.Rmd’ using rmarkdown Attaching package: 'rvest' The following object is masked from 'package:readr': guess_encoding Quitting from lines 53-63 (MW_ST000291_enrichment.Rmd) Error: processing vignette 'MW_ST000291_enrichment.Rmd' failed with diagnostics: there is no package called 'POMA' --- failed re-building ‘MW_ST000291_enrichment.Rmd’ --- re-building ‘MW_ST000629_enrichment.Rmd’ using rmarkdown Quitting from lines 53-62 (MW_ST000629_enrichment.Rmd) Error: processing vignette 'MW_ST000629_enrichment.Rmd' failed with diagnostics: there is no package called 'POMA' --- failed re-building ‘MW_ST000629_enrichment.Rmd’ --- re-building ‘food_enrichment_analysis.Rmd’ using rmarkdown metaboliteUniverse size: 300 metaboliteList size: 9 Warning: ggrepel: 143 unlabeled data points (too many overlaps). Consider increasing max.overlaps Warning: ggrepel: 143 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘food_enrichment_analysis.Rmd’ SUMMARY: processing the following files failed: ‘MW_ST000291_enrichment.Rmd’ ‘MW_ST000629_enrichment.Rmd’ Error: Vignette re-building failed. Execution halted