System dependencies not installed on Ubuntu 16.04

[jdblischak]

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I have run rhub::check_on_ubuntu() three times over the last few hours. Each time the R session stalls. Below is an example where I ran traceback() after killing the process.

> rhub::check_on_ubuntu()
─  Building package
─  Uploading package
─  Preparing build, see status at
   https://builder.r-hub.io/status/workflowr_1.6.2.tar.gz-df8b86d2788c48c78c3500725f6158b2
|^C
-^C
> traceback()
6: Sys.sleep(0.1)
5: make_streamer(private$ids_[[which]], make_status_parser)
4: check_livelog(self, private, which)
3: chk$livelog()
2: check(path = path, platform = check_shortcut_platforms$ubuntu, 
       ...)
1: rhub::check_on_ubuntu()

I didn't realize the jobs were running until the 3rd one, which sent me a PREPERROR email. The HTML version wasn't rendering for me, but I am able to (sometimes) load the plaintext logs:

• Build 1
• Build 2
• Build 3

It looks like multiple system dependencies are not being installed. Some copy-pasting from the log:

libgit2-dev wasn't installed:

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 libgit2-dev : Depends: libcurl4-gnutls-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

xml2 can't be installed because libxml2-dev wasn't installed:

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’

openssl can't be installed because libssl-dev wasn't installed:

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: [email protected] (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’

Potentially related: #357

[gaborcsardi]

It is the same as this issue: https://github.com/r-hub/sysreqsdb/issues/77

[gaborcsardi]

We'll update to Ubuntu 20.04 soon, that'll solve it.

[jdblischak]

@gaborcsardi Thanks for the quick response!

[jdblischak]

Any update on migrating to Ubuntu 20.04? I just ran into this problem again today when testing a different package. It's tricky because it stalls instead of failing. Even the plaintext log is unavailable (an example from today). If migrating to Ubuntu 20.04 is time-consuming, a temporary measure would be to check the recursive dependencies of the package, and fail early if any of the dependencies are known to be uninstallable on Ubuntu. I'm happy to help with this.

[jdblischak]

Update: I received emails for the Ubuntu jobs ~24 hours after I originally submitted them. Thus the link above in my previous message now works.

And the systems dependencies were able to be installed on Ubuntu 16.04:

+R-HUB-R-HUB-R-HUBsysreqs=export DEBIAN_FRONTEND=noninteractive; apt-get -y update && apt-get install -y libssl-dev libxml2-dev libcurl4-openssl-dev

And thus the R packages xml2, openssl, and curl were successfully installed.

[jdblischak]

Given that my recent jobs were able to install xml2 and openssl, I tried re-submitting workflowr. Confusingly it still continues to fail to install these packages:

https://builder.r-hub.io/status/workflowr_1.6.2.9000.tar.gz-d81d0f2555a44a2a9e1a37ebc1c6cad2

[gaborcsardi]

This issue is about the previous R-hub system, it does not apply to the new system, so I am closing it now. Please see https://r-hub.github.io/rhub/ for the new system, R-hub v2.