Error with install.packages using R v 3.5.1 and 3.5.2

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Error with install.packages using R v 3.5.1 and 3.5.2

Emily Wan
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}}

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Re: Error with install.packages using R v 3.5.1 and 3.5.2

Jeff Newmiller
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 <[hidden email]> 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.

______________________________________________
[hidden email] 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.
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Re: Error with install.packages using R v 3.5.1 and 3.5.2

Emily Wan
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 <[hidden email]>
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 <[hidden email]>
> 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}}

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Error with install.packages using R v 3.5.1 and 3.5.2

Jeff Newmiller
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 <[hidden email]> 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
><[hidden email]>
>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
><[hidden email]>
>> 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.

______________________________________________
[hidden email] 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.
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Re: Error with install.packages using R v 3.5.1 and 3.5.2

Henrik Bengtsson-5
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
<[hidden email]> 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 <[hidden email]> 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
> ><[hidden email]>
> >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
> ><[hidden email]>
> >> 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.
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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.
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Re: 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 <[hidden email]>
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
> <[hidden email]> 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 <
> [hidden email]> 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
> > ><[hidden email]>
> > >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
> > ><[hidden email]>
> > >> 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.
> >
> > ______________________________________________
> > [hidden email] 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.
>

--
The information in this e-mail is intended only for the ...{{dropped:18}}

______________________________________________
[hidden email] 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.