[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 The initial failure stated I had an outdated broom package, but updates are failing too, not just on broom, but on all packages, and there is no meaningful error output on the installation failures.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
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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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