DiffBind installation fails: Error: package ‘BiocGenerics’ 0.34.0 is loaded, but >= 0.36.0 is required by ‘IRanges’
0
0
Entering edit mode
tina • 0
@tina
Last seen 3.7 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
    ‘/tmp/RtmpPjlZTU/downloaded_packages’
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

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=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 • 3.4k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
1
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.

ADD REPLY

Login before adding your answer.

Traffic: 384 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6