[R] help finding a starting point to diagnose inability to install or update packages

Duncan Murdoch murdoch@dunc@n @end|ng |rom gm@||@com
Sun Apr 25 18:41:27 CEST 2021

On 25/04/2021 10:52 a.m., Larry Johnson wrote:
> Hi. Short version.  tidyverse disappeared from my packages, and won't install.  The initial failure stated I had an outdated broom package, but updates are failing too, not just on broom, but on all packages, and there is no meaningful error output on the installation failures.
> I typically use RStudio on Fedora 33, but the problem I'm about to describe occurs whether I use RStudio or the text version.
> To give you overview, here is the output from sessionInfo:
>> sessionInfo()
> R version 4.0.4 (2021-02-15)
> Platform: x86_64-redhat-linux-gnu (64-bit)
> Running under: Fedora 33 (Workstation Edition)
> Matrix products: default
> BLAS/LAPACK: /usr/lib64/libflexiblas.so.3.0
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
> loaded via a namespace (and not attached):
>   [1] htmlwidgets_1.5.3   colorspace_2.0-0    scales_1.1.1        compiler_4.0.4
>   [5] magrittr_2.0.1      R6_2.5.0            leaflet_2.0.4.1     htmltools_0.5.1.1
>   [9] tools_4.0.4         crosstalk_1.1.1     digest_0.6.27       lifecycle_1.0.0
> [13] munsell_0.5.0       rlang_0.4.10        CoprManager_0.3.7.1
> After trying complete reinstalls of R, RStudio, and the CRAN repositories here's the last error messages I've gotten in my attempts to install and load tidyverse:
>> install.packages(c("broom", "callr", "cli", "cpp11", "dbplyr", "haven", "highr", "knitr", "pillar", "processx", "RcppArmadillo", "reprex", "tibble", "tinytex", "vctrs", "viridis", "viridisLite", "withr"))
> Install system packages...
>> install.packages("tidyverse")
> Install system packages...
>> library(tidyverse)
> Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
>   namespace ‘broom’ 0.7.5 is being loaded, but >= 0.7.6 is required
> Attempts to install or update broom fail with no output.
> I've been searching for similar reports of failure here in these archives, on the RStudio forums, and on the internet and have found nothing that's a seamless match.  If I can't find anything I'll check out filing a bug report (I've never done it with R before).
> Any help with a starting point in diagnosing this will be appreciated.

Are you using install_github(), or otherwise installing non-CRAN 
versions?  If so, stop doing that. First, run update.packages(ask=FALSE)
to make sure you are up to date.  Then delete any package that is newer 
than the CRAN version, and reinstall it using the basic install.packages().

Here's code to compare versions:

CRAN <- available.packages()
here <- installed.packages()
for (i in seq_len(nrow(here))) {
   if (here[i, "Package"] %in% rownames(CRAN) &&
       package_version(here[i, "Version"]) >
         package_version(CRAN[here[i, "Package"], "Version"]))
     cat(here[i, c("Package", "Version")], "\n", sep=" " )

Duncan Murdoch

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