I'll put that in my notes. Thanks!
Larry Johnson Editor and Publisher Cobb County Courier 404-664-2034 http://cobbcountycourier.com ________________________________ From: Hadley Wickham <h.wick...@gmail.com> Sent: Sunday, April 25, 2021 7:14 PM To: Larry Johnson <larry.john...@cobbcountycourier.com> Cc: Duncan Murdoch <murdoch.dun...@gmail.com>; r-help@r-project.org <r-help@r-project.org> Subject: Re: [R] help finding a starting point to diagnose inability to install or update packages If this happens again in the future, you might try the development version of pak: install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/";) pak::pak("tidyverse") pak automatically diagnoses a number of common problems that causes install.packages() to fail. Hadley On Sun, Apr 25, 2021 at 4:51 PM Larry Johnson <larry.john...@cobbcountycourier.com> wrote: > > It was pointed out to me by Jeff Newmiller that I should have been hitting > "reply all" so that others could see the thread and make comment, > corrections, or benefit from any solution. > > So, I'm going to summarize the end result. > > Duncan Murdoch walked me through some diagnostic steps, and what ultimately > worked was to run > > remove.packages("broom") > install.packages("broom") > > and then repeat that for each of the four packages that attempts to load > tidyverse indicated had dependency issues (I know that last sentence was > ungrammatical, but you probably get my drift). > > I'd still like to know why updating packages in bulk isn't working for me, > but I can move ahead for now, and I'll figure out how to fix that later. > > So thanks Duncan. > > > Larry Johnson > > Editor and Publisher > > Cobb County Courier > > 404-664-2034 > > http://cobbcountycourier.com > > ________________________________ > From: Duncan Murdoch <murdoch.dun...@gmail.com> > Sent: Sunday, April 25, 2021 12:41 PM > To: Larry Johnson <larry.john...@cobbcountycourier.com>; r-help@r-project.org > <r-help@r-project.org> > Subject: Re: [R] help finding a starting point to diagnose inability to > install or update packages > > 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 The initial failure stated I had an outdated broom package, but 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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- http://hadley.nz [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
