[R-pkg-devel] Build process generated non-portable files

[Dirk Eddelbuettel]

On 17 August 2024 at 17:22, Ivan Krylov via R-package-devel wrote:
| В Fri, 16 Aug 2024 18:53:55 +0000
| anj5xsj9 using nilly.addy.io пишет:
| 
| > In the past other packages have failed to build and not only on the
| > intel container see
| > "https://github.com/SpeakEasy-2/speakeasyR/actions/runs/10202337528/job/28226219457"
| > where several containers failed at the setup-deps step. There is
| > overlap in which package fails (i.e. protGenerics and sparseArray
| > fail in multiple containers but succeed in others while in one
| > container ExperimentHub fails). It seems the only packages failing
| > are from Bioconductor. Assume this is a bioconductor or pak issue.
| 
| Could also be an rhub issue, although unlike the igraph problem below,
| I have no idea where to start diagnosing it.
| 
| > > > igraph::sample_pref(10)  
| > > Error in dyn.load(file, DLLpath = DLLpath, ...) :
| > >  unable to load shared object
| > > '/root/R/x86_64-pc-linux-gnu-library/4.5/igraph/libs/igraph.so':
| > > libopenblasp.so.0: cannot open shared object file: No such file or
| > > directory  
| > 
| > I.e. the same error with building targets. I can raise an issue on
| > rigraph as well.
| 
| This is a problem with the binary package used by rhub. If you
| reinstall the source package from CRAN instead of
| https://github.com/r-hub/repos and
| https://github.com/cran/igraph/releases/, it will work, but take much
| more time compiling the package:
| 
| options(repos = getOption('repos')['CRAN'])
| install.packages('igraph')

The r2u binaries can offer help here for running on Ubuntu. They are a
'superset' of the same p3m binaries but aim to (and generally manage to)
provide working binaries. I just validated via a Docker container running it:

edd using rob:~$ docker run --rm -ti rocker/r2u:jammy bash
root using 64a8b23a9bc7:/# install.r igraph    # install.packages() works too
[ ... log of installation of 14 binaries omitted here ... ]
root using 64a8b23a9bc7:/# R

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> library(igraph)

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> 


Best, Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org