Larry Johnson
2021-Apr-25 21:50 UTC
[R] help finding a starting point to diagnose inability to install or update packages
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.duncan at gmail.com>
Sent: Sunday, April 25, 2021 12:41 PM
To: Larry Johnson <larry.johnson at cobbcountycourier.com>; r-help at
r-project.org <r-help at 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 The initial failure stated I had an outdated broom package, but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]]
Hadley Wickham
2021-Apr-25 23:14 UTC
[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.johnson at 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.duncan at gmail.com>
> Sent: Sunday, April 25, 2021 12:41 PM
> To: Larry Johnson <larry.johnson at cobbcountycourier.com>; r-help at
r-project.org <r-help at 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]]
>
> ______________________________________________
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
--
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