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

[Emily Wan]

Henrik and Jeff -
Thank you both for your thoughts and helpful suggestions on this problem -
a colleague and I did some forensics on this end and discovered the issue
was related to a combination of 1) slow network connections and 2) having
my personal library installed on a different server from where R was
installed.  When we reassigned the libPath() to the "local drive" (same
virtual machine that R was installed on - after getting write permissions
for that drive), the issue was resolved.
Thank you both for your responses!

On Wed, Jan 16, 2019 at 2:42 PM Henrik Bengtsson <henrik.bengtsson using gmail.com>
wrote:

> 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
> <jdnewmil using 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 <
> reesw using 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
> > ><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.
> > >>
> >
> > --
> > Sent from my phone. Please excuse my brevity.
> >
> > ______________________________________________
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>

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