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

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

Larry Johnson
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  The initial failure stated I had an outdated broom package, but updates are failing too, not just on broom, but on all packages, and there is no meaningful error output on the installation failures.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]]

______________________________________________
[hidden email] 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.
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Re: help finding a starting point to diagnose inability to install or update packages

Duncan Murdoch-2
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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Re: help finding a starting point to diagnose inability to install or update packages

Jeff Newmiller
In reply to this post by Larry Johnson
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 <[hidden email]> 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]]
>
>______________________________________________
>[hidden email] 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.

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[hidden email] 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.
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Re: help finding a starting point to diagnose inability to install or update packages

Larry Johnson
In reply to this post by Duncan Murdoch-2
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 <[hidden email]>
Sent: Sunday, April 25, 2021 12:41 PM
To: Larry Johnson <[hidden email]>; [hidden email] <[hidden email]>
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]]

______________________________________________
[hidden email] 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.
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Re: help finding a starting point to diagnose inability to install or update packages

hadley wickham
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
<[hidden email]> 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 <[hidden email]>
> Sent: Sunday, April 25, 2021 12:41 PM
> To: Larry Johnson <[hidden email]>; [hidden email] <[hidden email]>
> 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]]
>
> ______________________________________________
> [hidden email] 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

______________________________________________
[hidden email] 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.
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Re: help finding a starting point to diagnose inability to install or update packages

Larry Johnson
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 <[hidden email]>
Sent: Sunday, April 25, 2021 7:14 PM
To: Larry Johnson <[hidden email]>
Cc: Duncan Murdoch <[hidden email]>; [hidden email] <[hidden email]>
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
<[hidden email]> 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 <[hidden email]>
> Sent: Sunday, April 25, 2021 12:41 PM
> To: Larry Johnson <[hidden email]>; [hidden email] <[hidden email]>
> 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]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
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> 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

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______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.