openssl not found in Ubuntu and Fedora builds.

[JSchoenbachler]

Other users and I have noted some issues with the linux rhub platforms as of late, see this issue: r-hub/rhub#508

I'm not sure of the exact details for the other users, but in my situation openssl isn't found on the platform which causes R packages that use openssl to fail.
One of my runs with the relevant line:
https://builder.r-hub.io/status/zeitzeiger_2.0.4.tar.gz-18424e001248437e88769f36486e4b92#L4429

I looked through your Dockerfiles and see that it should be installing:

rhub-linux-builders/ubuntu/Dockerfile

Line 37 in 18a40ad

libcurl4-openssl-dev \

Not sure why it isn't. Also not sure if this happens on other linux builds, as I only tested with "Ubuntu Linux 20.04.1 LTS, R-release, GCC" and "Fedora Linux, R-devel, clang, gfortran".

Also a minor point, but your README and other documentation list the Ubuntu version as 16.04 even though the version being used is 20.04.

[JSchoenbachler]

@gaborcsardi Hey Sorry to ping you, you're just the last person to push to this repository. Was wondering if you guys were aware of this bug?

I'm trying to check several packages on rhub to submit to CRAN and am running into this issue.

[gaborcsardi]

Sorry about that. The logs are not kept for log, can you please resubmit the package and then ping me here? Thanks.

[JSchoenbachler]

@gaborcsardi I just ran it on the original package I got the error with and another package that relies on a similar package that uses openssl-

• zeitzeiger (original Package):
  • Windows: https://builder.r-hub.io/status/zeitzeiger_2.0.4.tar.gz-6dbbcc13f4dc4f96a48a8db033680b39
  • Ubuntu: https://builder.r-hub.io/status/zeitzeiger_2.0.4.tar.gz-c51c0195a8524217bd05755fc649ec78
  • Fedora: https://builder.r-hub.io/status/zeitzeiger_2.0.4.tar.gz-09696dd5c8574ed8a79d20845ae871de
• limorhyde (different package):
  • Windows: https://builder.r-hub.io/status/limorhyde_1.0.1.tar.gz-dc150820b77d4ee4b2c707c73ea603b2
  • Ubuntu: https://builder.r-hub.io/status/limorhyde_1.0.1.tar.gz-4d85eecdf97b47e5a3451f92324e1774
  • Fedora: https://builder.r-hub.io/status/limorhyde_1.0.1.tar.gz-4e771157e50c4d16b4cd22b5e61ecf7b

Some weird notes:

• zeitzeiger (the first package noticed on) suceeds with a NOTE on Windows but fails with PREPERROR on Ubuntu and Fedora.
• limorhyde succeeds with ERROR on Windows, Ubuntu, and Fedora. I think these succeed rather than failing with the PREPERROR due to some way something is referenced in the package.

[gaborcsardi]

The ssl error happens because your package depends on openssl through a Bioconductor package, and we don't automatically discover system dependencies of Bioconductor package. I have added an exception for this now here: r-hub/sysreqsdb@5fd38f9 so it should work now.

[JSchoenbachler]

Okay thank you! I appreciate it.

[gaborcsardi]

And a similar exception seems to be needed for annotate to make the other package pick up openssl: r-hub/sysreqsdb@2780892
So please try that again as well.

[gaborcsardi]

The error on Windows is a bug in install.packages(), it cannot work out the proper installation order if a mixture of binary and source packages are involved. There isn't much that we can do about this, unfortunately. Eventually Bioconductor will ship binary packages for R 4.2.x Windows, but until then this is not going to work.

[JSchoenbachler]

@gaborcsardi This all looks fine now except that it looks like I'm now having the same problem with xml2-config on Ubuntu only:

https://builder.r-hub.io/status/zeitzeiger_2.0.4.tar.gz-fbb965ad7c0a4e81b4634119082a81e4

[gaborcsardi]

Yeah, libxml2 is also need through BioC:

❯ pak::pkg_deps_explain("local::.", "XML")
zeitzeiger -> sva -> genefilter -> annotate -> XML

It should work now: r-hub/sysreqsdb@3f42c7b

[JSchoenbachler]

@gaborcsardi excellent, everything is working now!

Is adding the ability to discover BioConductor system dependencies a possible future enhancement? That way it these situations don't pop up and require exceptions.

Regardless thanks for helping out with this issue!

[JSchoenbachler]

Hey @gaborcsardi sorry to bother you again.

I'm running into a similar issue to this again on a different package. Could you take a look and see if it's the same thing?

Windows: https://builder.r-hub.io/status/limorhyde_1.0.1.tar.gz-9416d81d2e2b45f3af64f3664b5c59ee
Ubuntu: https://builder.r-hub.io/status/limorhyde_1.0.1.tar.gz-6c16435c56e04d78a38de6188e280984

Strangely enough, doesn't seem to happen on Fedora:
https://builder.r-hub.io/status/limorhyde_1.0.1.tar.gz-0cdd17258f1f4c1e801c6465bc87137b

[gaborcsardi]

Yes, annotate also needs XML -> libxml2, it seems: r-hub/sysreqsdb@85f3558

Should be good now. (Except for R-devel on Windows, which will not work for the same reason as before.)

[JSchoenbachler]

@gaborcsardi (Really sorry to keep pinging you) could you also do this for the package it's happening to here: https://builder.r-hub.io/status/limorhyde2_0.0.6.tar.gz-2a69a89258d8447488fbd161c365cddc