Bug 239169
| Summary: | math/R package needs readline (rl_sort_completion_matches) | ||
|---|---|---|---|
| Product: | Ports & Packages | Reporter: | Nicola Mingotti <nmingotti> |
| Component: | Individual Port(s) | Assignee: | Joseph Mingrone <jrm> |
| Status: | Closed Not A Bug | ||
| Severity: | Affects Some People | CC: | pkg, rhurlin, xenomorph |
| Priority: | --- | Flags: | bugzilla:
maintainer-feedback?
(jrm) |
| Version: | Latest | ||
| Hardware: | Any | ||
| OS: | Any | ||
|
Description
Nicola Mingotti
2019-07-12 16:56:23 UTC
Hi Nicola,
This is strange. The R package should depend on devel/readline. To confirm this, I just started a clean jail and built the package.
# pkg info -d R | grep readline
readline-8.0.0
# pkg info -r readline | grep R
readline-8.0.0:
R-3.6.0_1
Next, I removed all packages from the jail, set pkg to use the default repository and installed the default R package. I see the same as above, that is, R depends on readline.
Could you provide more hints as to why your installation of R did not depend on readline?
Regards,
Joseph
(In reply to Joseph Mingrone from comment #1) Hi Joseph, Luckily i was able to reproduce the exact same behaviour in another system I have. My first test was on: $> uname -a FreeBSD fbs-slacmac 12.0-RELEASE FreeBSD 12.0-RELEASE r341666 GENERIC amd64 My second test is in: $> uname -a FreeBSD nise1 12.0-RELEASE FreeBSD 12.0-RELEASE r341666 GENERIC amd64 All commands from here are in machine nise1. #> pkg info | grep readline readline-7.0.5 #> pkg install R #> R ld-elf.so.1: /usr/local/lib/R/lib/libR.so.3.6: Undefined symbol "rl_sort_completion_matches" #> pkg info | grep readline readline-7.0.5 #> pkg install readline # this updates the readline #> R ==> Now works #> pkg info | grep readline readline-8.0.0 In conclusion, if there is readline-7.X already installed in the system, the new one will not be installed with R, and R will not work with the old one. bye Nicola Thanks for clarifying. 1. Are you using the official packages? 2. Based on your command snippets below, I assume you have not `pkg lock`ed any packages? I confirmed your issue by running a little test in a jail. Unfortunately I can't see a problem with math/R itself, since it depends on devel/readline [1]. It's more of a 'feature/limitation' of the ports tree and pkg. I'll dig a little deeper and see if I can provide more information. [1] More specifically, it has USES=readline:port, which in turn has LIB_DEPENDS+=libreadline.so.8:devel/readline. Adding pkg@ because I am unclear if it is expected behavior for `pkg install R` to ignore the missing libreadline.so.8 library dependency. I would have guessed that pkg would either complain or try to upgrade the readline package to version 8.0.0. A summary of the problem: - Start with an older version of the readline package installed, version 7.0.5. - `pkg install R`, which requires the shared library libreadline.so.8 - Installing R does not complain or try to upgrade the readline package - R fails to run I found this page looking for why R wouldn't run. Count me in as an impacted user! No locked packages. # uname -a FreeBSD hostname.local 12.0-RELEASE-p7 FreeBSD 12.0-RELEASE-p7 GENERIC amd64 # pkg install R # R ld-elf.so.1: /usr/local/lib/R/lib/libR.so.3.6: Undefined symbol "rl_sort_completion_matches" # pkg install redline redline gets upgraded from 7.0.5 to 8.0.0, and then R runs. Closing this as it's not an issue with math/R and it's not a bug, but simply a current limitation with our packages. Package repositories are meant to work as a set (a snapshot of the repository at any given time). This means one-off installations or upgrades are not supported. In this case you would have to do a `pkg upgrade` before `pkg install R`. |
