[Bioc-devel] package named spdeq causes error

[Levi Waldron]

Looking further up the list of error messages, there is a long dependency
chain ending with a missing system dependency (see below):
   * anamiR -> agricolae -> spdep -> sf -> system dependency libgdal-dev

You should be able to fix it with `apt install libgdal-dev` if you're on
Debian/Ubuntu. BTW, I figured this out on a Docker+Singularity container
and scripts I've been working on to try to make almost all of Bioconductor
installable, to make it easier to run release+devel side by side, and to
smooth the edges for people who don't feel like learning the million flags
Docker has or where their package and home directories go every time they
restart :). I'll add libgal-dev. It's early but see
https://github.com/waldronlab/bioconductor_devel if you want to try, and I
really welcome feedback on documentation or functionality.

Dependency error chain:

* installing *source* package ‘sf’ ...

** package ‘sf’ successfully unpacked and MD5 sums checked

configure: CC: gcc

configure: CXX: g++ -std=gnu++11

*checking for gdal-config... no*

*no*

*configure: error: gdal-config not found or not executable.*

*ERROR: configuration failed for package ‘sf’*

* removing ‘/usr/local/lib/R/host-site-library/sf’

* installing *source* package ‘minfi’ ...

** R

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (minfi)

* installing *source* package ‘klaR’ ...

** package ‘klaR’ successfully unpacked and MD5 sums checked

** R

** data

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded

* DONE (klaR)

*ERROR: dependency ‘sf’ is not available for package ‘spdep’*

** removing ‘/usr/local/lib/R/host-site-library/spdep’*

* installing *source* package ‘methylumi’ ...

** R

** data

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (methylumi)

*ERROR: dependency ‘spdep’ is not available for package ‘agricolae’*

* removing ‘/usr/local/lib/R/host-site-library/agricolae’

* installing *source* package ‘lumi’ ...

** R

** data

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (lumi)

ERROR: dependency ‘agricolae’ is not available for package ‘anamiR’

* removing ‘/usr/local/lib/R/host-site-library/anamiR’


The downloaded source packages are in

‘/tmp/RtmpOjPTFv/downloaded_packages’

Warning messages:

1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :

  installation of package ‘sf’ had non-zero exit status

2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :

  installation of package ‘spdep’ had non-zero exit status

3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :

  installation of package ‘agricolae’ had non-zero exit status

4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :

  installation of package ‘anamiR’ had non-zero exit status

> *


On Thu, Feb 21, 2019 at 11:00 PM Dario Strbenac <dstr7320 using uni.sydney.edu.au>
wrote:

> Good day,
>
> I don't, but your software package imports agricolae which imports spdep.
> spdep is available from CRAN, so it's strange that the Bioconductor build
> server running Linux has not been able to install it.
>
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Levi Waldron
http://www.waldronlab.io
Associate Professor of Biostatistics    CUNY School of Public Health
US: +1 646-364-9616                                           Skype:
levi.waldron

	[[alternative HTML version deleted]]