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. -- The information in this e-mail is intended only for the ...{{dropped:18}}
Jeff Newmiller
2019-Jan-15 21:51 UTC
[R] Error with install.packages using R v 3.5.1 and 3.5.2
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.
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. >-- The information in this e-mail is intended only for the ...{{dropped:18}}