Error with install.packages using R v 3.5.1 and 3.5.2
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 at 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 at 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 at 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 at 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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