I tried rerunning some old (6 months) code processing RNAseq data that had previously run just fine. Now it is getting hung up importing Salmon quants using tximeta, with the following error:

sample_table$files <- file.path(dir, sample_table$names, "quant.sf")
file.exists(sample_table$files)
se <- tximeta(sample_table)

[1] TRUE

[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, : bad value

I tried downgrading from vroom_1.6.4 to vroom_1.6.3, which oddly worked once, but then threw the same error. After re-updating vroom, the error persists.

I see a fix on this site for tximport, but when I opened the tximeta function I didn't see a line to change the importer, so was hesitant to mess with it.

Any idea how to solve this? Thanks!

• Miles

sessionInfo( )

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.5.2

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago tzcode source: internal

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] fgsea_1.26.0 enrichplot_1.20.3 clusterProfiler_4.8.3 ggrepel_0.9.3 broom_1.0.5 ggpubr_0.6.0 qvalue_2.32.0
[8] viridis_0.6.4 viridisLite_0.4.2 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.3 purrr_1.0.2
[15] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.3 tidyverse_2.0.0 org.Mm.eg.db_3.17.0 genefilter_1.82.1
[22] apeglm_1.22.1 PoiClaClu_1.0.2.1 RColorBrewer_1.1-3 pheatmap_1.0.12 vsn_3.68.0 ensembldb_2.24.1 AnnotationFilter_1.24.0
[29] GenomicFeatures_1.52.2 AnnotationDbi_1.62.2 rhdf5_2.44.0 DESeq2_1.40.2 SummarizedExperiment_1.30.2 Biobase_2.60.0 MatrixGenerics_1.12.3
[36] matrixStats_1.0.0 GenomicRanges_1.52.1 GenomeInfoDb_1.36.4 IRanges_2.34.1 S4Vectors_0.38.2 BiocGenerics_0.46.0 tximeta_1.18.3

loaded via a namespace (and not attached): [1] splines_4.3.1 later_1.3.1 BiocIO_1.10.0 bitops_1.0-7 ggplotify_0.1.2 filelock_1.0.2
[7] polyclip_1.10-6 preprocessCore_1.62.1 XML_3.99-0.14 lifecycle_1.0.3 rstatix_0.7.2 vroom_1.6.3
[13] lattice_0.21-8 MASS_7.3-60 backports_1.4.1 magrittr_2.0.3 limma_3.56.2 rmarkdown_2.25
[19] yaml_2.3.7 httpuv_1.6.11 cowplot_1.1.1 DBI_1.1.3 abind_1.4-5 zlibbioc_1.46.0
[25] ggraph_2.1.0 RCurl_1.98-1.12 yulab.utils_0.1.0 tweenr_2.0.2 rappdirs_0.3.3 GenomeInfoDbData_1.2.10
[31] tidytree_0.4.5 annotate_1.78.0 codetools_0.2-19 DelayedArray_0.26.7 DOSE_3.26.2 xml2_1.3.5
[37] ggforce_0.4.1 tidyselect_1.2.0 aplot_0.2.2 farver_2.1.1 BiocFileCache_2.8.0 GenomicAlignments_1.36.0
[43] jsonlite_1.8.7 ellipsis_0.3.2 tidygraph_1.2.3 survival_3.5-7 bbmle_1.0.25 tools_4.3.1
[49] progress_1.2.2 treeio_1.24.3 Rcpp_1.0.11 glue_1.6.2 gridExtra_2.3 xfun_0.40
[55] numDeriv_2016.8-1.1 withr_2.5.1 BiocManager_1.30.22 fastmap_1.1.1 rhdf5filters_1.12.1 fansi_1.0.5
[61] digest_0.6.33 timechange_0.2.0 R6_2.5.1 mime_0.12 gridGraphics_0.5-1 colorspace_2.1-0
[67] GO.db_3.17.0 biomaRt_2.56.1 RSQLite_2.3.1 utf8_1.2.3 generics_0.1.3 data.table_1.14.8
[73] rtracklayer_1.60.1 prettyunits_1.2.0 graphlayouts_1.0.1 httr_1.4.7 S4Arrays_1.0.6 scatterpie_0.2.1
[79] pkgconfig_2.0.3 gtable_0.3.4 blob_1.2.4 XVector_0.40.0 shadowtext_0.1.2 htmltools_0.5.6.1
[85] carData_3.0-5 ProtGenerics_1.32.0 scales_1.2.1 png_0.1-8 ggfun_0.1.3 knitr_1.44
[91] rstudioapi_0.15.0 tzdb_0.4.0 reshape2_1.4.4 rjson_0.2.21 coda_0.19-4 nlme_3.1-163
[97] curl_5.1.0 bdsmatrix_1.3-6 cachem_1.0.8 BiocVersion_3.17.1 parallel_4.3.1 HDO.db_0.99.1
[103] restfulr_0.0.15 pillar_1.9.0 grid_4.3.1 vctrs_0.6.3 promises_1.2.1 car_3.1-2
[109] dbplyr_2.3.4 xtable_1.8-4 tximport_1.28.0 evaluate_0.22 mvtnorm_1.2-3 cli_3.6.1
[115] locfit_1.5-9.8 compiler_4.3.1 Rsamtools_2.16.0 rlang_1.1.1 crayon_1.5.2 ggsignif_0.6.4
[121] emdbook_1.3.13 affy_1.78.2 plyr_1.8.9 fs_1.6.3 stringi_1.7.12 BiocParallel_1.34.2
[127] munsell_0.5.0 Biostrings_2.68.1 lazyeval_0.2.2 GOSemSim_2.26.1 Matrix_1.6-1.1 hms_1.1.3
[133] patchwork_1.1.3 bit64_4.0.5 Rhdf5lib_1.22.1 KEGGREST_1.40.1 shiny_1.7.5 interactiveDisplayBase_1.38.0 [139] AnnotationHub_3.8.0 igraph_1.5.1 memoise_2.0.1 affyio_1.70.0 ggtree_3.8.2 fastmatch_1.1-4
[145] bit_4.0.5 downloader_0.4 ape_5.7-1 gson_0.1.0

```

Not sure what you mean by 'a line to change the importer', but it's an argument that gets passed in via the ellipsis ...

se <- tximeta(sample_table, importer = read.delim)