DiffBind installation fails: Error: package ‘BiocGenerics’ 0.34.0 is loaded, but >= 0.36.0 is required by ‘IRanges’
Entering edit mode
tina • 0
Last seen 2.6 years ago

Hi all, I'm having trouble loading ‘BiocGenerics’ >= 0.36.0. I don't understand why given that I'm using R 4.0.0 and appropriate Bioconductor release (https://bioconductor.org/news/bioc_3_11_release/) .

> BiocManager::install("DiffBind")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'DiffBind'
also installing the dependency ‘systemPipeR’

trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/systemPipeR_1.22.0.tar.gz'
Content type 'application/x-gzip' length 2728246 bytes (2.6 MB)
downloaded 2.6 MB

trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/DiffBind_2.16.2.tar.gz'
Content type 'application/x-gzip' length 2040129 bytes (1.9 MB)
downloaded 1.9 MB

* installing *source* package ‘systemPipeR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘BiocGenerics’ 0.34.0 is loaded, but >= 0.36.0 is required by ‘IRanges’
Execution halted
ERROR: lazy loading failed for package ‘systemPipeR’
* removing ‘<path>R/x86_64-pc-linux-gnu-library/4.0/systemPipeR’
ERROR: dependency ‘systemPipeR’ is not available for package ‘DiffBind’
* removing ‘<path>/R/x86_64-pc-linux-gnu-library/4.0/DiffBind’

The downloaded source packages are in
Installation path not writeable, unable to update packages: AnnotationDbi,
  AnnotationHub, ape, backports, BH, BiocFileCache, biomaRt, bit, bit64, broom,
  callr, caTools, ChAMP, cli, clipr, clue, clusterGeneration, coda, colorspace,
  covr, cowplot, cpp11, crosstalk, data.table, DBI, dbplyr, deldir, dendextend,
  devtools, digest, DMRcate, doParallel, dplyr, DT, e1071, emmeans,
  ExperimentHub, fansi, fastmap, fitdistrplus, forcats, foreach, Formula,
  future, future.apply, generics, GetoptLong, ggalluvial, ggdendro, ggfittext,
  ggplot2, ggraph, ggrepel, ggridges, gh, git2r, globals, glue, gplots,
  graphlayouts, gridGraphics, hexbin, Hmisc, hms, htmlTable, htmltools,
  htmlwidgets, httpuv, igraph, inline, isoband, iterators, jsonlite, knitr,
  labeling, leiden, lmtest, loo, lubridate, magrittr, matrixStats, mclust,
  memoise, openssl, openxlsx, patchwork, pbapply, pillar, pkgbuild, plotly,
  plotrix, prettydoc, processx, ps, R.methodsS3, R.oo, R.utils, R6, rappdirs,
  Rcpp, RcppAnnoy, RcppArmadillo, RcppEigen, readr, reprex, reticulate, rhdf5,
  rlang, rmarkdown, rprojroot, RSQLite, rstudioapi, sass, sctransform, Seurat,
  shiny, shinythemes, spatstat.data, spatstat.utils, StanHeaders, statmod,
  stringdist, stringi, testthat, tibble, tidyr, tinytex, usethis, uwot, V8,
  vctrs, vegan, VGAM, withr, xfun, boot, class, codetools, foreign, KernSmooth,
  MASS, Matrix, mgcv, nlme, nnet, spatial, survival
Warning messages:
1: In install.packages(...) :
  installation of package ‘systemPipeR’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘DiffBind’ had non-zero exit status

sessionInfo( )
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.0      tools_4.0.0

I can't quite tell what's going on, given that dependencies for version 0.36.0 are R>=4.0.0 https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html

When try to install BiocManager::install("BiocGenerics") to see what's going on, it immediately attempts 0.34.0 version. What's going on

> BiocManager::install("BiocGenerics")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'BiocGenerics'

trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/BiocGenerics_0.34.0.tar.gz'
Content type 'application/x-gzip' length 46859 bytes (45 KB)
downloaded 45 KB

* installing *source* package ‘BiocGenerics’ ...
#<cut off>
systemPipeR Bioconductor DiffBind BiocGenerics • 2.5k views
Entering edit mode

Current Bioc is 3.12, not 3.11, see https://www.bioconductor.org/install/

Entering edit mode

Update your Bioconductor version BiocManager::install(version = "3.12"). Make sure that the update succeeds BiocManager::valid(). It looks like one of the paths is not writeable, maybe because the packages were installed with an 'administrator' account; if you're the administrator, I'd undo that, installing only base R as administrator.

The problem reported is with IRanges, and I'd guess, in your current installation, BiocManager::valid() would report that IRanges was 'too new', suggesting that some non-standard procedure was used to install IRanges; re-installing (in a new session) IRanges would likely revert to the old version, and allow you to continue using Bioconductor version 3.11 if that were what you wanted to do, e.g., for reproducibility.


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