[Bioc-devel] Cannot install Bioconductor packages with biocLite() after loading QuasR

[Pariksheet Nanda]

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