Re: [R] Error with install.packages using R v 3.5.1 and 3.5.2
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 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 > 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 > > > > > >wrote: > > > > > >> Please ask questions about Bioconductor on the Bioconductor forum > > >[1]. > > >> > > >> Chances are that you need to re-install Bioconductor because packages > > >are > > >> in
Re: [R] Error with install.packages using R v 3.5.1 and 3.5.2
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 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 > 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}} __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error with install.packages using R v 3.5.1 and 3.5.2
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}} __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.