Installing rlang version 1.1.0

Question

[Medha]

I was trying to install ExomeDepth package, after that one of its command from its document getBamCounts gives following error.

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace ‘rlang’ 1.0.5 is already loaded, but >= 1.1.0 is required
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace ‘rlang’ 1.0.5 is already loaded, but >= 1.1.0 is required
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace ‘rlang’ 1.0.5 is already loaded, but >= 1.1.0 is required

First thing that I do not understand is that it should have installed the version it is saying on its own. Even so, I tried installing 1.1.0 using following install.packages("rlang", version="1.1.0") . But it still installs 1.0.5. I checked if the 1.1.0 is available or not using

av <- available.packages(filters=list())
av[av[, "Package"] == "rlang", ]

               Package    Version       Priority        Depends        Imports       LinkingTo
    rlang    "rlang"        "1.1.0"          NA       "R (>= 3.5.0)"      "utils"            NA       
    rlang    "rlang"        "1.0.6"          NA       "R (>= 3.4.0)"      "utils"            NA       
               Suggests                                                                                                                                                     
    rlang    "cli (>= 3.1.0), covr, crayon, fs, glue, knitr, magrittr,\nmethods, pillar, rmarkdown, stats, testthat (>= 3.0.0), tibble,\nusethis, vctrs (>= 0.2.3), withr"
    rlang    "cli (>= 3.1.0), covr, crayon, fs, glue, knitr, magrittr,\nmethods, pillar, rmarkdown, stats, testthat (>= 3.0.0), tibble,\nusethis, vctrs (>= 0.2.3), withr"
              Enhances License                   License_is_FOSS License_restricts_use
    rlang      "winch"  "MIT + file LICENSE" NA              NA                   
    rlang      "winch"  "MIT + file LICENSE" NA              NA                   
              OS_type   Archs                           MD5sum                             NeedsCompilation File
    rlang           NA      NA          "58861e9d99517eb10f7683249efae513"      "yes"                  NA  
    rlang           NA      NA          "907bc04039194b0c7edc19e9084b14fc"      "yes"                  NA  
              Repository                               
    rlang "https://cloud.r-project.org/src/contrib"
    rlang "https://cran.microsoft.com/src/contrib"

Can someone tell me how to install rlang v1.1.0?

Answer 1

[Lluís R.]

Having a package duplicated means they are at a different .libPaths() sites. Check which version is in which directory and directly remove the version 1.0.6 or use remove.packages("rlang", lib.loc = .libPaths()[x]). Then you will be able to continue using and installing packages normally.

[Medha]

EDIT: "It is resolved now" Thansk Lluís R. with your advice, I took out the reason for duplication, I was installing rlang 1.1.0 after installing ExomeDepth, so I reversed this by installing rlang 1.1.0 before installing ExomeDepth. Thanks.

Lluís R.

I want to install ExomeDepth, these dependencies were not getting installed on its own so I installed it before installing ExomeDepth install.packages("BiocManager")

BiocManager::install(c("Biostrings", "IRanges", "Rsamtools", "GenomicRanges", "GenomicAlignments"))

These got installed at

The downloaded source packages are in ‘/tmp/RtmpueWuwX/downloaded_packages’

Now I installed ExomeDepth: devtools::install_github("vplagnol/ExomeDepth") . Witjhin this the rlang is shown to install in this:

 installing *source* package ‘rlang’ ...

 installing to /local_disk0/.ephemeral_nfs/envs/rEnv-a66fb82e-9d00-4573-99f2-0ce76799030d/00LOCK-rlang/00new/rlang/libs

Then it showed in the end this:

  The downloaded source packages are in
  ‘/tmp/Rtmp7JiAL9/downloaded_packages’
  * checking for file ‘/tmp/Rtmp7JiAL9/remotes44847bac8a0/vplagnol-ExomeDepth-d642cbd/DESCRIPTION’ ... OK
  * preparing ‘ExomeDepth’:
  * checking DESCRIPTION meta-information ... OK
  * cleaning src
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * looking to see if a ‘data/datalist’ file should be added
  * building ‘ExomeDepth_1.1.16.tar.gz’

Installing package into ‘/local_disk0/.ephemeral_nfs/envs/rEnv-a66fb82e-9d00-4573-99f2-0ce76799030d’ (as ‘lib’ is unspecified)

Now I am installing this:

install.packages("rlang", version="1.1.0")

packageVersion("rlang")

This gives the path

  The downloaded source packages are in
  ‘/tmp/Rtmp7JiAL9/downloaded_packages’

Is the method you mentioned will help out here too?

[Lluís R.]

When you edited the comment I didn't receive any notification. One thing is where a package is downloaded and where it is finally installed. install.packages doesn't have a version argument. You might be using a different package or not getting what you thought.