tidyverse not loading; xml2 and rvest failing

[tckosvic]

I can't get tidyverse to install. modules xml2 and rvest are failing to load properly. Root of the problem seems to be that package: libicui18n.so.58 is not being found and is needed for them. That file is not in R packages as far as I can see. Why is it not there?

I found libicui18n.so.58 in another app (anaconda python). Where do I put it so R finds it?

Using R version 4.3. RStudio 2023.06.2.

Another question is are the modules of tidyverse that perhaps were loaded, while xml2 and rvet were not, are they operational?

thanks, tom kosvic

[Gabor]

So you are using R from conda? Then the best is to install R packages from conda as well.

Or you are using a non-conda R while conda is active? Then the best is to de-activate conda while you are using R.

[tckosvic]

I was unaware of any connection between R and conda. After seeing your comment and looking it up, though, it looks like they can be used together in an R environment in anaconda. I do not have such a setup. So I am not using R from conda.

Where do I put the libicui18n.so.58 from anaconda into R so it can be found?

thanks, tom kosvic

[Gabor]

Non-conda R does not work with the conda libraries in general. This is why you need to deactivate conda while using non-conda R.

Here is a longer explanation why: igraph failing to compile due to missing libgfortran.so.4 (Arch based Linux) · Issue #275 · igraph/rigraph · GitHub

If you are on a platform that rig supports, I would suggest

1. deactivating conda
2. installing rig
3. installing R with rig.

See GitHub - r-lib/rig: The R Installation Manager

[tckosvic]

@gabor, you were right. I deactivated conda. tidyverse installed completely in R terminal window. It was also available as library in Rstudio. There were some conflicts that I do not yet know anything about yet.
See below for code from RStudio::

> library(tidyverse)
── Attaching core tidyverse packages ─────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.3     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ stringr   1.5.0
✔ ggplot2   3.4.3     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.0
✔ purrr     1.0.2     
── Conflicts ───────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package to force all conflicts to become errors
>

If anyone has insights as to what these mean let me know.

I had no idea tidyverse was a conda library as you indicated. Nothing I saw said there was a conda/R relationship.

I used my previously installed R and did not look into rig. I will look at rig to see if I should remove R and reinstall.

thanks, tom kosvic

[FJCC]

The conflicts listed when loading tidyverse are perfectly normal. It just means, for instance, that the dpylr package has a filter() function and so does the stats package. When you load dplyr, the filter function in stats is "masked" so that you have to call it with a reference to the stats package included, stats::filter(). Calling simply filter() gives you the function from dplyr.