Package updates fail: how to fix the causes

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Package updates fail: how to fix the causes

Rich Shepard
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

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Re: Package updates fail: how to fix the causes

Bert Gunter-2
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 <[hidden email]>
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
>
> ______________________________________________
> [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.
>

        [[alternative HTML version deleted]]

______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
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Re: Package updates fail: how to fix the causes

Ista Zahn
In reply to this post by Rich Shepard
Hi Rich,

Install udunits. If you don't know how to do that in slackware go ask
on a slackware forum.

Best,
Ista

On Fri, Feb 15, 2019 at 10:58 AM Rich Shepard <[hidden email]> 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
>
> ______________________________________________
> [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: Package updates fail: how to fix the causes

Rich Shepard
In reply to this post by Bert Gunter-2
On Fri, 15 Feb 2019, Bert Gunter wrote:

> 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.

Bert,

   Since I run only Slackware I'm not seeing how posting on a debian or
fedora mail list would help. Those two distributions were part of the error
messasge when 'units' didn't build.

Regards,

Rich

______________________________________________
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Re: Package updates fail: how to fix the causes

Rich Shepard
In reply to this post by Ista Zahn
On Fri, 15 Feb 2019, Ista Zahn wrote:

> Install udunits. If you don't know how to do that in slackware go ask on a
> slackware forum.

Ista,

Interesting. This must be a new dependency because prior versions of units
didn't require it. However, SlackBuilds.org has that package so I'll install
it then work my way down the list of failed updates.

Thanks for the pointer,

Rich

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Re: Package updates fail: how to fix the causes [FIXED]

Rich Shepard
In reply to this post by Ista Zahn
On Fri, 15 Feb 2019, Ista Zahn wrote:

> Install udunits.

Ista,

Yep. Installing that package allowed the chain to build. Much appreciated.

Best regards,

Rich

______________________________________________
[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.