Question

Problem to update packages

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ajaz240792 ▴ 10

@ajaz240792-21380

Last seen 2.5 years ago

Spain

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
    ‘/tmp/Rtmpoz9kNt/downloaded_packages’
**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 • 939 views

ADD COMMENT • link updated 5.5 years ago by Martin Morgan 25k • written 5.5 years ago by ajaz240792 ▴ 10

Martin Morgan · Answer 1 · 2019-07-28

1

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Martin Morgan 25k

@martin-morgan-1513

Last seen 5 months ago

United States

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 COMMENT • link 5.5 years ago Martin Morgan 25k

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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 REPLY • link updated 5.5 years ago by Martin Morgan 25k • written 5.5 years ago by ajaz240792 ▴ 10

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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)[ is.na(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 REPLY • link 5.5 years ago Martin Morgan 25k