[R] Error with install.packages using R v 3.5.1 and 3.5.2

[Emily Wan]

Hi Jeff -
I do not think the issue is Bioconductor (which is why I had posted the
inquiry on this forum - but as an aside, I do have the latest version of
Bioconductor (3.8)).   As an example, when I attempt to use the generic
install.packages() function, I receive the same error message. I have
included an example below (along with the sessionInfo):

> install.packages('stringr')
Installing package into ‘~/My Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
also installing the dependencies ‘glue’, ‘magrittr’
trying URL '
https://cran.revolutionanalytics.com/bin/windows/contrib/3.5/glue_1.3.0.zip'
Content type 'application/zip' length 108591 bytes (106 KB)
downloaded 106 KB
trying URL '
https://cran.revolutionanalytics.com/bin/windows/contrib/3.5/magrittr_1.5.zip
'
Content type 'application/zip' length 155452 bytes (151 KB)
downloaded 151 KB
trying URL '
https://cran.revolutionanalytics.com/bin/windows/contrib/3.5/stringr_1.3.1.zip
'
Content type 'application/zip' length 194247 bytes (189 KB)
downloaded 189 KB
Error in if (any(diff)) { : missing value where TRUE/FALSE needed
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2
>
Please let me know what additional information is needed - many thanks.

On Tue, Jan 15, 2019 at 4:51 PM Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
wrote:

> Please ask questions about Bioconductor on the Bioconductor forum [1].
>
> Chances are that you need to re-install Bioconductor because packages are
> installed in two-digit version-specific libraries... e.g. R 3.4 and R 3.5
> do not share packages.
>
> [1] https://support.bioconductor.org
>
> On January 15, 2019 11:51:16 AM PST, Emily Wan <reesw using channing.harvard.edu>
> wrote:
> >Hi -
> >I am working with R on a Window Server 2012 R2 - I had originally
> >installed
> >R (v3.5.1) in September/October 2018 and have used multiple packages
> >without incident. However, last week, when attempting to install
> >additional
> >packages (using install.packages() or Bioconductor's
> >BiocManager::install()
> >wrapper), I kept on receiving the following error message:
> >
> >Error in if (any(diff)) { : missing value where TRUE/FALSE needed
> >
> >I have searched the prior threads on this topic (including the issue
> >reported with R v3.4.0 which required a patch), rebooted my server, and
> >actually uninstalled R v3.5.1 and upgraded to v3.5.2 but am still
> >receiving
> >the same error message when I attempt to install *any* package.
> >Please let me know what additional details I can provide to assist with
> >troubleshooting. Thank you.
>
> --
> Sent from my phone. Please excuse my brevity.
>

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