[R] Package updates fail: how to fix the causes

[Bert Gunter]

You *might* do better posting this on r-sig-debian and/or r-sig-fedora,
especially as this is not a question about R programming per se, which
makes it off topic for this list, but more on topic for those lists.

Cheers,
Bert

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Fri, Feb 15, 2019 at 7:58 AM Rich Shepard <rshepard using appl-ecosys.com>
wrote:

> Running R-3.5.2 on Slackware-14.2, using my script that updates installed
> packages found four that failed. My web searches did not find relevant
> hits,
> and only the last build failure is explained by the build failure of a
> specific dependency. The results displayed are:
>
> ERROR: dependency ‘sf’ is not available for package ‘spdep’
> * removing ‘/usr/lib/R/library/spdep’
>
> The downloaded source packages are in
>         ‘/tmp/RtmpzEBBCY/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning messages:
> 1: In install.packages(update[instlib == l, "Package"], l, contriburl =
> contriburl,  :
>    installation of package ‘units’ had non-zero exit status
> 2: In install.packages(update[instlib == l, "Package"], l, contriburl =
> contriburl,  :
>    installation of package ‘later’ had non-zero exit status
> 3: In install.packages(update[instlib == l, "Package"], l, contriburl =
> contriburl,  :
>    installation of package ‘sf’ had non-zero exit status
> 4: In install.packages(update[instlib == l, "Package"], l, contriburl =
> contriburl,  :
>    installation of package ‘spdep’ had non-zero exit status
>
> Starting at the top, trying to install 'units' resulted in identifying a
> missing library:
>
> Configuration failed because libudunits2.so was not found. Try installing:
>      * deb: libudunits2-dev (Debian, Ubuntu, ...)
>      * rpm: udunits2-devel (Fedora, EPEL, ...)
>      * brew: udunits (OSX)
>    If udunits2 is already installed in a non-standard location, use:
>      --configure-args='--with-udunits2-lib=/usr/local/lib'
>    if the library was not found, and/or:
>      --configure-args='--with-udunits2-include=/usr/include/udunits2'
>    if the header was not found, replacing paths with appropriate values.
>    You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.
>
> --------------------------------------------------------------------------------
> See `config.log' for more details
> ERROR: configuration failed for package ‘units’
> * removing ‘/usr/lib/R/library/units’
>
> The downloaded source packages are in
>         ‘/tmp/RtmprbnasH/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning message:
> In install.packages("units") :
>    installation of package ‘units’ had non-zero exit status
>
> Please advise me on how to proceed so these four packages are eventually
> updated or re-installed.
>
> TIA,
>
> Rich
>
> ______________________________________________
> R-help using 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.
>

	[[alternative HTML version deleted]]