Question: Problem to update packages
gravatar for ajaz240792
4 months ago by
ajaz24079210 wrote:

I am on Linux Ubuntu version 3.6.1, using BiocManager version 3.9. When I install any package of Bioconductor, at the final of the installation I get the following message:

The downloaded source packages are in
**installation path not writeable,** **unable to update packages**: abind, acepack, askpass, assertthat, backports,
  base64enc, BH, bitops, broom, caTools, cellranger, cli, clipr, colorspace, crayon, crosstalk, curl,
  data.table, DBI, estimability, fansi, forcats, foreach, Formula, gbm, generics, glue, gridExtra, gtable,
  highr, Hmisc, htmlTable, htmltools, htmlwidgets, httpuv, httr, iterators, jsonlite, kernlab, labeling,
  later, latticeExtra, lazyeval, lme4, lubridate, magrittr, manipulateWidget, maptools, MatrixModels, miniUI,
  minqa, ModelMetrics, modelr, munsell, nloptr, nortest, pbkrtest, pkgconfig, pkgKitten, plogr, plyr,
  prettyunits, prodlim, promises, ps, purrr, quantreg, R6, RcmdrMisc, RColorBrewer, RcppEigen, readr,
  readstata13, readxl, relimp, rematch, reshape2, rstudioapi, sandwich, scales, selectr, sourcetools, sp,
  SparseM, SQUAREM, stringi, stringr, tcltk2, tidyr, tidyselect, tidyverse, timeDate, utf8, viridis,
  viridisLite, webshot, whisker, withr, xml2, xtable, yaml, zeallot, class, codetools, foreign, KernSmooth,
  lattice, Matrix, mgcv, nnet, rpart, spatial, survival

I need support to know how to update these packages.

update problem • 142 views
ADD COMMENTlink modified 4 months ago by Martin Morgan ♦♦ 24k • written 4 months ago by ajaz24079210
Answer: Problem to update packages
gravatar for Martin Morgan
4 months ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

These packages were installed to a library under a different account, e.g., by a system administrator. The person with access to that account would need to update them.

The output of .libPaths() indicates the paths where libraries are installed; installed.packages() returns information about which packages are installed in which libraries. One can manage, using the guidance on ?.libPaths and assuming that the packages have not been installed in R's default library, to have complete control over the libraries that you see during your session.

ADD COMMENTlink written 4 months ago by Martin Morgan ♦♦ 24k

Hello friend and thanks for your advice.

I figured out the problem

I only had to update using the terminal of the system instead of using RStudio.

The command inside the terminal were

$ sudo R
$ BiocManager::install()
$ a
ADD REPLYlink written 4 months ago by ajaz24079210

When you use sudo you are running as administrator; I would strongly discourage installing packages, other than base R, as administrator.

If this is your own system, then my suggestion would be to remove all packages from the location they are currently in

$ sudo R
> pkgs = installed.packages()
> rm = rownames(pkgs)[[, "Priority"]) ]
> writeLines(rm, "~/pkgs_to_install.txt")
> remove.packages(rm)
> q()

and start again installing packages as a regular user

$ R
> pkgs_to_install = readLines("~/pkgs_to_install.txt")
> BiocManager::install(pkgs_to_install)
ADD REPLYlink modified 4 months ago • written 4 months ago by Martin Morgan ♦♦ 24k
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