Hi folks, It looks like loading QuasR breaks biocLite() because it magically wants to use biocLite() in qAlign():
$ find -not -name '*.Rnw' -exec grep -E '(BiocInstaller|biocLite)' {} + 2>/dev/null ./DESCRIPTION: S4Vectors (>= 0.9.25), IRanges, BiocInstaller, Biobase, ./R/qAlign.R: biocLite(genome, suppressUpdates=TRUE, lib=lib.loc) ./NAMESPACE:importFrom(BiocInstaller, biocLite) $ Here's the error in a fresh R session: > suppressPackageStartupMessages(library(QuasR)) > BiocInstaller::biocLite("BSgenome.Hsapiens.UCSC.hg38") Error: failed to update BiocInstaller: namespace ‘BiocInstaller’ is imported by ‘QuasR’ so cannot be unloaded > What would be a good way to fix this? I think trying to use biocLite() from inside a package is a bit naughty and installing packages should be left up to the user instead? Reproducible in R 3.4.1 and a daily build: > sessionInfo() R Under development (unstable) (2017-08-01 r73012) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.3 LTS Matrix products: default BLAS: /share/apps/spack/opt/spack/linux-ubuntu16-x86_64/gcc-5.4.0/r-2017-08-01-jyjbn6hodegfxzvg6aojsdu7fmrdzi3y/rlib/R/lib/libRblas.so LAPACK: /share/apps/spack/opt/spack/linux-ubuntu16-x86_64/gcc-5.4.0/r-2017-08-01-jyjbn6hodegfxzvg6aojsdu7fmrdzi3y/rlib/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] QuasR_1.17.0 Rbowtie_1.17.0 GenomicRanges_1.29.12 [4] GenomeInfoDb_1.13.4 IRanges_2.11.12 S4Vectors_0.15.6 [7] BiocGenerics_0.23.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.12 RColorBrewer_1.1-2 [3] BiocInstaller_1.27.3 compiler_3.5.0 [5] XVector_0.17.1 prettyunits_1.0.2 [7] progress_1.1.2 GenomicFeatures_1.29.8 [9] bitops_1.0-6 GenomicFiles_1.13.10 [11] tools_3.5.0 zlibbioc_1.23.0 [13] biomaRt_2.33.4 digest_0.6.12 [15] bit_1.1-12 BSgenome_1.45.1 [17] RSQLite_2.0 memoise_1.1.0 [19] tibble_1.3.4 lattice_0.20-35 [21] rlang_0.1.2 Matrix_1.2-11 [23] DelayedArray_0.3.19 DBI_0.7 [25] GenomeInfoDbData_0.99.1 hwriter_1.3.2 [27] stringr_1.2.0 rtracklayer_1.37.3 [29] Biostrings_2.45.4 bit64_0.9-7 [31] grid_3.5.0 Biobase_2.37.2 [33] R6_2.2.2 AnnotationDbi_1.39.2 [35] XML_3.98-1.9 BiocParallel_1.11.6 [37] latticeExtra_0.6-28 magrittr_1.5 [39] blob_1.1.0 Rsamtools_1.29.1 [41] matrixStats_0.52.2 GenomicAlignments_1.13.5 [43] ShortRead_1.35.1 assertthat_0.2.0 [45] SummarizedExperiment_1.7.5 stringi_1.1.5 [47] RCurl_1.95-4.8 VariantAnnotation_1.23.8 > Pariksheet --- Pariksheet Nanda PhD Candidate in Genetics and Genomics System Administrator, Storrs HPC Cluster University of Connecticut _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel