Hi! I got a note about failing for InTAD package only in Bioc-devel version: http://bioconductor.org/checkResults/devel/bioc-LATEST/InTAD/machv2-buildsrc.html
Notably, there were no changes to the package before this error started occurring thus I suppose it might be connected to some updates in other packages. To reproduce the issue I installed the latest available R-devel version and also switched to bioconductor-devel. Installing the package worked OK. Error message from report was the following: Quitting from lines 93-94 (InTAD.Rmd) Error: processing vignette 'InTAD.Rmd' failed with diagnostics: missing value where TRUE/FALSE needed --- failed re-building ‘InTAD.Rmd’ The problem seems to be occurring in creating the object ( https://github.com/kokonech/InTAD/blob/master/vignettes/InTAD.Rmd ): *inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel,mbAnnData)* However, I did not observe any issues in package installation. Moreover, I managed to build the vignette without problems simply running the following command from latest source: *rmarkdown::render('InTAD/vignettes/InTAD.Rmd') * Any suggestions how I could reproduce and fix this error? Below I also included my sessionInfo() Best regards, Konstantin *R Under development (unstable) (2020-12-26 r79698)Platform: x86_64-pc-linux-gnu (64-bit)Running under: openSUSE Leap 42.3Matrix products: defaultBLAS: /home/okonechn/B080/okonechn/tools/R-devel/lib/libRblas.soLAPACK: /home/okonechn/B080/okonechn/tools/R-devel/lib/libRlapack.solocale:[1] Cattached base packages:[1] parallel stats4 stats graphics grDevices utils datasets[8] methods baseother attached packages: [1] BiocStyle_2.19.1 InTAD_1.11.0 [3] MultiAssayExperiment_1.17.2 SummarizedExperiment_1.21.1 [5] Biobase_2.51.0 MatrixGenerics_1.3.0 [7] matrixStats_0.57.0 GenomicRanges_1.43.1 [9] GenomeInfoDb_1.27.3 IRanges_2.25.6[11] S4Vectors_0.29.6 BiocGenerics_0.37.0loaded via a namespace (and not attached): [1] tidyr_1.1.2 splines_4.1.0 carData_3.0-4 [4] BiocManager_1.30.10 GenomeInfoDbData_1.2.4 cellranger_1.1.0 [7] Rsamtools_2.7.0 yaml_2.2.1 pillar_1.4.7[10] backports_1.2.1 lattice_0.20-41 glue_1.4.2[13] digest_0.6.27 ggsignif_0.6.0 XVector_0.31.1[16] qvalue_2.23.0 colorspace_2.0-0 htmltools_0.5.0[19] Matrix_1.3-0 plyr_1.8.6 XML_3.99-0.5[22] pkgconfig_2.0.3 broom_0.7.3 haven_2.3.1[25] bookdown_0.21 zlibbioc_1.37.0 purrr_0.3.4[28] scales_1.1.1 openxlsx_4.2.3 rio_0.5.16[31] BiocParallel_1.25.2 tibble_3.0.4 farver_2.0.3[34] generics_0.1.0 car_3.0-10 ggplot2_3.3.2[37] ellipsis_0.3.1 ggpubr_0.4.0 magrittr_2.0.1[40] crayon_1.3.4 readxl_1.3.1 mclust_5.4.7[43] evaluate_0.14 rstatix_0.6.0 forcats_0.5.0[46] foreign_0.8-81 tools_4.1.0 data.table_1.13.4[49] hms_0.5.3 BiocIO_1.1.2 lifecycle_0.2.0[52] stringr_1.4.0 munsell_0.5.0 zip_2.1.1[55] DelayedArray_0.17.7 Biostrings_2.59.2 compiler_4.1.0[58] rlang_0.4.9 grid_4.1.0 RCurl_1.98-1.2[61] rjson_0.2.20 labeling_0.4.2 rmarkdown_2.6[64] bitops_1.0-6 restfulr_0.0.13 gtable_0.3.0[67] abind_1.4-5 curl_4.3 reshape2_1.4.4[70] R6_2.5.0 GenomicAlignments_1.27.2 knitr_1.30[73] dplyr_1.0.2 rtracklayer_1.51.2 stringi_1.5.3[76] Rcpp_1.0.5 vctrs_0.3.6 xfun_0.19[79] tidyselect_1.1.0* [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
