Error with Graphics API version since I upgraded my R version

[AlejRSosa]

Hello, I am not sure if this is the place to comment, but I have been trying to contact someone who could shed some light as to how solve this problem.

I have upgraded my R version as it kept prompting me to do so and ever since I cannot use RnBeads anymore as when I try to run a differential methylation analysis it throws this error:

2023-03-27 17:56:09 16.7 STATUS STARTED Quality Control Section 2023-03-27 18:12:00 12.7 STATUS Added sequencing coverage histograms 2023-03-27 18:16:16 18.7 WARNING ReportGgPlot error ('off' method): Graphics API version mismatch Error in f(...) : Graphics API version mismatch In addition: Warning messages: 1: In options(stringsAsFactors = TRUE) : 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled 2: The dot-dot notation (..count..) was deprecated in ggplot2 3.4.0. ℹ Please useafter_stat(count)instead. ℹ The deprecated feature was likely used in the RnBeads package. Please report the issue to the authors. This warning is displayed once every 8 hours. Calllifecycle::last_lifecycle_warnings()to see where this warning was generated.

I have used RnBeads not too long ago for an analysis that I must replicate asap, and now I find that it is not working all of a sudden. I have thought of uninstalling R and RStudio and reinstalling it but I don't know if that would work?

This is the command I used, by the way:

analysis <- rnb.run.analysis(dir.reports=report.dir, sample.sheet=sample.annotation, data.source=bed.dir, data.type="bs.bed.dir")

[schmic05]

Hi @AlejRSosa From your error message, I cannot directly tell what the issue might be, because it only shows warning messages and not errors. I think re-installing RnBeads might do the trick, but I am not sure about it. If you could share the full analysis log and also the output of sessionInfo() I might have clearer idea.

[AlejRSosa]

Hi, Here is my first analysis log LOG_FAILEDRUN.log

I also downgraded my R version as all of this started when I upgraded my R version. I downgraded to a version that I know works for someone else in my lab and ran the analysis again and it is still giving me the same exact error. I attach the .log file for that one too which is named analysis.log analysis.log

My session info is: `R version 4.2.1 (2022-06-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.2 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale: [1] LC_CTYPE=en_IE.UTF-8 LC_NUMERIC=C LC_TIME=en_IE.UTF-8 LC_COLLATE=en_IE.UTF-8
[5] LC_MONETARY=en_IE.UTF-8 LC_MESSAGES=en_IE.UTF-8 LC_PAPER=en_IE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] shinyjs_2.1.0 shiny_1.7.4
[3] RnBeads.hg19_1.30.0 RnBeads_2.16.0
[5] plyr_1.8.6 methylumi_2.44.0
[7] minfi_1.44.0 bumphunter_1.40.0
[9] locfit_1.5-9.7 iterators_1.0.14
[11] foreach_1.5.2 Biostrings_2.66.0
[13] XVector_0.38.0 SummarizedExperiment_1.28.0
[15] MatrixGenerics_1.10.0 FDb.InfiniumMethylation.hg19_2.2.0
[17] org.Hs.eg.db_3.16.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [19] GenomicFeatures_1.50.4 AnnotationDbi_1.60.2
[21] reshape2_1.4.4 scales_1.2.1
[23] Biobase_2.58.0 illuminaio_0.40.0
[25] matrixStats_0.61.0 limma_3.54.2
[27] gridExtra_2.3 gplots_3.1.1
[29] ggplot2_3.3.5 fields_14.1
[31] viridis_0.6.2 viridisLite_0.4.0
[33] spam_2.9-1 ff_4.0.9
[35] bit_4.0.4 cluster_2.1.2
[37] MASS_7.3-55 GenomicRanges_1.50.2
[39] GenomeInfoDb_1.34.9 IRanges_2.32.0
[41] S4Vectors_0.36.2 BiocGenerics_0.44.0

loaded via a namespace (and not attached): [1] systemfonts_1.0.4 BiocFileCache_2.6.1 splines_4.2.1 BiocParallel_1.32.6
[5] digest_0.6.29 htmltools_0.5.5 fansi_1.0.2 magrittr_2.0.2
[9] memoise_2.0.1 tzdb_0.3.0 readr_2.1.4 annotate_1.76.0
[13] askpass_1.1 siggenes_1.72.0 prettyunits_1.1.1 colorspace_2.0-2
[17] blob_1.2.2 rappdirs_0.3.3 textshaping_0.3.6 dplyr_1.1.1
[21] crayon_1.5.0 RCurl_1.98-1.12 genefilter_1.80.3 GEOquery_2.66.0
[25] survival_3.2-13 glue_1.6.1 gtable_0.3.0 zlibbioc_1.44.0
[29] DelayedArray_0.24.0 Rhdf5lib_1.20.0 maps_3.4.0 HDF5Array_1.26.0
[33] DBI_1.1.2 rngtools_1.5.2 Rcpp_1.0.8 xtable_1.8-4
[37] progress_1.2.2 mclust_5.4.9 preprocessCore_1.60.2 dotCall64_1.0-2
[41] httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2 farver_2.1.0
[45] pkgconfig_2.0.3 reshape_0.8.9 XML_3.99-0.9 dbplyr_2.1.1
[49] utf8_1.2.2 labeling_0.4.2 later_1.3.0 tidyselect_1.2.0
[53] rlang_1.1.0 munsell_0.5.0 tools_4.2.1 cachem_1.0.6
[57] cli_3.6.1 generics_0.1.2 RSQLite_2.2.9 stringr_1.5.0
[61] fastmap_1.1.0 ragg_1.2.1 yaml_2.3.5 bit64_4.0.5
[65] beanplot_1.3.1 caTools_1.18.2 scrime_1.3.5 purrr_1.0.1
[69] KEGGREST_1.38.0 nlme_3.1-155 doRNG_1.8.6 sparseMatrixStats_1.10.0 [73] mime_0.12 nor1mix_1.3-0 xml2_1.3.3 biomaRt_2.54.1
[77] compiler_4.2.1 rstudioapi_0.13 filelock_1.0.2 curl_4.3.2
[81] png_0.1-7 tibble_3.2.1 stringi_1.7.6 lattice_0.20-45
[85] Matrix_1.5-3 multtest_2.54.0 vctrs_0.6.1 pillar_1.9.0
[89] lifecycle_1.0.3 rhdf5filters_1.10.0 data.table_1.14.2 bitops_1.0-7
[93] httpuv_1.6.5 rtracklayer_1.58.0 R6_2.5.1 BiocIO_1.8.0
[97] promises_1.2.0.1 KernSmooth_2.23-20 codetools_0.2-18 gtools_3.9.2
[101] assertthat_0.2.1 rhdf5_2.42.0 openssl_1.4.6 rjson_0.2.21
[105] withr_2.5.0 GenomicAlignments_1.34.1 Rsamtools_2.14.0 GenomeInfoDbData_1.2.9
[109] hms_1.1.1 quadprog_1.5-8 tidyr_1.3.0 base64_2.0.1
[113] DelayedMatrixStats_1.20.0 restfulr_0.0.15 `

[schmic05]

Okay, so the issue seems to be with your graphics device. Maybe you can try to follow the instructions here: https://stackoverflow.com/questions/68753250/getting-the-error-graphics-api-version-mismatch

Otherwise, as you sugggested earlier, a re-install of R and all packages might be required. The error seems not to come from RnBeads directly.