Immediately after you get that error:
Error in if (any(diff)) { : missing value where TRUE/FALSE needed
what does
> traceback()
output? (I suspect this error occurs in tools:::checkMD5sums() used
to assert that the package files are correctly downloaded). Also,
going forward, let's try with a single package installed, e.g.
install.packages("glue"). Does that also give an error?
/Henrik
On Wed, Jan 16, 2019 at 11:10 AM Jeff Newmiller
<jdnew...@dcn.davis.ca.us> wrote:
>
> I don't know specifically where that error comes from... but I can think of
> two possible directions to go:
>
> 1) If you have ever run R as Administrator then you may need to delete your
> personal library (‘~/My Documents/R/win-library/3.5’) and reload all packages
> NOT using Run As Administrator. Any files created by R using those security
> credentials may impede the function of R when run without those credentials.
>
> 2) There have previously been reports that this error arises from the
> installed.packages function that is invoked by install.packages. This could
> be related to (1) above or be unrelated. You might confirm on this discussion
> thread whether this function runs okay for you.
>
> For future reference, use CRAN packages for examples on this mailing list to
> clarify that the problem is relevant here.
>
> On January 16, 2019 9:48:12 AM PST, Emily Wan <re...@channing.harvard.edu>
> wrote:
> >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
> ><jdnew...@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
> ><re...@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.
> >>
>
> --
> Sent from my phone. Please excuse my brevity.
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
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