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rama.pranadi
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@ramapranadi-22768
Last seen 4.7 years ago
Hi,
I am receiving this error when trying to use tximeta():
> se <- tximeta(coldata)
importing quantifications
reading in files with read_tsv
1 2 3
found matching transcriptome:
[ GENCODE - Mus musculus - release M24 ]
loading existing TxDb created: 2020-01-26 06:20:01
Error in dbFileConnect(file) :
DB file '/Users/ramapranadinata/Library/Caches/BiocFileCache/291456c9cd_291456c9cd.sqlite' not found
is it supposed to find the BiocFileCache.sqlite file?
Thanks!
-------------------------------
Traceback()
> traceback()
5: stop("DB file '", dbfile, "' not found")
4: dbFileConnect(file)
3: loadDb(loadpath)
2: getTxDb(txomeInfo)
1: tximeta(coldata)
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.2
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices
[6] utils datasets methods base
other attached packages:
[1] AnnotationHub_2.18.0 BiocFileCache_1.10.2
[3] dbplyr_1.4.2 tximeta_1.4.3
[5] pheatmap_1.0.12 RColorBrewer_1.1-2
[7] DESeq2_1.26.0 SummarizedExperiment_1.16.1
[9] DelayedArray_0.12.2 BiocParallel_1.20.1
[11] matrixStats_0.55.0 Biobase_2.46.0
[13] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0
[15] IRanges_2.20.2 S4Vectors_0.24.3
[17] BiocGenerics_0.32.0 forcats_0.4.0
[19] stringr_1.4.0 dplyr_0.8.3
[21] purrr_0.3.3 readr_1.3.1
[23] tidyr_1.0.2 tibble_2.1.3
[25] ggplot2_3.2.1 tidyverse_1.3.0
[27] tximport_1.14.0 tximportData_1.14.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-1
[2] htmlTable_1.13.3
[3] XVector_0.26.0
[4] base64enc_0.1-3
[5] fs_1.3.1
[6] rstudioapi_0.10
[7] bit64_0.9-7
[8] interactiveDisplayBase_1.24.0
[9] AnnotationDbi_1.48.0
[10] fansi_0.4.1
[11] lubridate_1.7.4
[12] xml2_1.2.2
[13] splines_3.6.2
[14] geneplotter_1.64.0
[15] knitr_1.27
[16] Formula_1.2-3
[17] jsonlite_1.6
[18] Rsamtools_2.2.1
[19] broom_0.5.3
[20] annotate_1.64.0
[21] cluster_2.1.0
[22] png_0.1-7
[23] shiny_1.4.0
[24] BiocManager_1.30.10
[25] compiler_3.6.2
[26] httr_1.4.1
[27] backports_1.1.5
[28] fastmap_1.0.1
[29] assertthat_0.2.1
[30] Matrix_1.2-18
[31] lazyeval_0.2.2
[32] cli_2.0.1
[33] later_1.0.0
[34] prettyunits_1.1.1
[35] acepack_1.4.1
[36] htmltools_0.4.0
[37] tools_3.6.2
[38] gtable_0.3.0
[39] glue_1.3.1
[40] GenomeInfoDbData_1.2.2
[41] rappdirs_0.3.1
[42] Rcpp_1.0.3
[43] cellranger_1.1.0
[44] vctrs_0.2.2
[45] Biostrings_2.54.0
[46] nlme_3.1-143
[47] rtracklayer_1.46.0
[48] xfun_0.12
[49] rvest_0.3.5
[50] mime_0.8
[51] lifecycle_0.1.0
[52] ensembldb_2.10.2
[53] XML_3.99-0.3
[54] zlibbioc_1.32.0
[55] scales_1.1.0
[56] promises_1.1.0
[57] ProtGenerics_1.18.0
[58] hms_0.5.3
[59] AnnotationFilter_1.10.0
[60] yaml_2.2.0
[61] curl_4.3
[62] memoise_1.1.0
[63] gridExtra_2.3
[64] biomaRt_2.42.0
[65] rpart_4.1-15
[66] latticeExtra_0.6-29
[67] stringi_1.4.5
[68] RSQLite_2.2.0
[69] BiocVersion_3.10.1
[70] genefilter_1.68.0
[71] checkmate_1.9.4
[72] GenomicFeatures_1.38.1
[73] rlang_0.4.3
[74] pkgconfig_2.0.3
[75] bitops_1.0-6
[76] lattice_0.20-38
[77] GenomicAlignments_1.22.1
[78] htmlwidgets_1.5.1
[79] bit_1.1-15.1
[80] tidyselect_0.2.5
[81] magrittr_1.5
[82] R6_2.4.1
[83] generics_0.0.2
[84] Hmisc_4.3-0
[85] DBI_1.1.0
[86] pillar_1.4.3
[87] haven_2.2.0
[88] foreign_0.8-75
[89] withr_2.1.2
[90] survival_3.1-8
[91] RCurl_1.98-1.1
[92] nnet_7.3-12
[93] modelr_0.1.5
[94] crayon_1.3.4
[95] progress_1.2.2
[96] jpeg_0.1-8.1
[97] locfit_1.5-9.1
[98] grid_3.6.2
[99] readxl_1.3.1
[100] data.table_1.12.8
[101] blob_1.2.1
[102] reprex_0.3.0
[103] digest_0.6.23
[104] xtable_1.8-4
[105] httpuv_1.5.2
[106] openssl_1.4.1
[107] munsell_0.5.0
[108] askpass_1.1
Just to be clear, you should use bfcremove() to remove the entry, not removing any files manually.
Thank you for the prompt response Michael. I am trying to download the BioFileCache package and run into this error. This was a pretty large error message so I hope what I provided is enough. Many thanks in advance for any help on this as well!
Ive actually been having the same problem when trying to install 'mygene' and 'annotate' packages. E.g. Error from trying to install mygene package (see below).
Error:
For one thing, tximeta depends on BiocFileCache so you shouldn’t need to re-install. It cannot install without BFC.
Also, you genetally can say “no” to build from source.
Thank you so much for the guidance/help. All fixed!
Regards, Rama