potential Bug in R 3.5.0

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potential Bug in R 3.5.0

Jochen Wirsing
Hello,
I am using R under Win7 and Antergos. After installing R 3.5.0 I ran into
several issues regarding gfortran not working properly and packages not
installing properly when requiring dependencies (which is quite often the case
when you have to reinstall all packages for the new R version).
Unfortunately, I cannot reproduce the gfortran issue at the moment (occuring
under Antergos), but regarding the depency-issue, https://pastebin.com/
0nU5n3pH shows one instance of the problem, when using "tidyverse". Adding
"dependencies = TRUE" does not help. Manual installation of packages (in the
right order and if an error occurs due to missing dependencies installing
those packages first) works, but is extremely time consuming and inconvenient.

Also, knitr does not acknowledge packages, even though they are called for
(using library() in the same code chunk) and therefore cannot compile code
properly.

All this happened only after upgrading to 3.5.0 and I hope those major issues
can be fixed soon.

Thank you very much!
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Re: potential Bug in R 3.5.0

Jeroen Ooms
On Sun, Jun 24, 2018 at 8:41 PM, Jochen Wirsing <[hidden email]> wrote:
> Hello,
> I am using R under Win7 and Antergos. After installing R 3.5.0 I ran into
> several issues regarding gfortran not working properly and packages not
> installing properly when requiring dependencies (which is quite often the case
> when you have to reinstall all packages for the new R version).
> Unfortunately, I cannot reproduce the gfortran issue at the moment (occuring
> under Antergos), but regarding the depency-issue, https://pastebin.com/
> 0nU5n3pH shows one instance of the problem, when using "tidyverse". Adding
> "dependencies = TRUE" does not help.

It looks like R thinks those packages (‘dbplyr’, ‘rvest’, ‘xml2’) are
already installed, but is unable to load them. I have never used
'Antergos' but could it be that those packages were installed with R
3.4 and therefore stopped working after you upgraded to R 3.5? You
need to rebuild all R packages after you update to R. The easiest way
is to run:

  update.packages(ask = F, checkBuilt = T)

Also check your .libPaths() to make sure that there are no old
packages left behind in older directories.

If this is not the issue, try finding out where those packages live
using e.g. find.packages("xml2") and see what error you get when
trying to load them with library("xml2").

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