Larry Johnson
2021-Apr-25 14:52 UTC
[R] help finding a starting point to diagnose inability to install or update packages
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 The initial failure stated I had an outdated broom package, but updates are failing too, not just on broom, but on all packages, and there is no meaningful error output on the installation failures.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. Thanks, ?Larry Johnson Editor and Publisher Cobb County Courier 404-664-2034 http://cobbcountycourier.com [[alternative HTML version deleted]]
Duncan Murdoch
2021-Apr-25 16:41 UTC
[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
Jeff Newmiller
2021-Apr-25 16:47 UTC
[R] help finding a starting point to diagnose inability to install or update packages
These are all contributed packages... don't file a bug report on R. Also,
tidyverse is a rediculously sprawling meta-package that seems prone to faulty
dependency data.
If you have a oroblem getting the right version of broom then focus on solving
that. One possibility is that your CRAN mirror is not up-to-date.. try a
different one or wait a few days for the updates to prooagate. Sometimes all it
takes is to update or re-install the offending package. If you want to push the
envelope you can use devtools::install_github or similar to bypass CRAN, but it
is possible that that version had a problem identified in the CRAN review that
you might have trouble with.
Whst is your options("repos") set to?
On April 25, 2021 7:52:28 AM PDT, Larry Johnson <larry.johnson at
cobbcountycourier.com> 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.
>
>Thanks,
>
>
>?Larry Johnson
>
>Editor and Publisher
>
>Cobb County Courier
>
>404-664-2034
>
>http://cobbcountycourier.com
>
> [[alternative HTML version deleted]]
>
>______________________________________________
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