I would like to release my R code under GPL-3. The code depends on a package 
(lme4) that itself uses "GPL >= 2", but which has upstream dependencies (minqa, 
numDeriv, rbibutils) that are GPL-2 only.  According to what I've read (see 
below), GPL-2 and GPL-3 are incompatible. Are the GPL-2 upstream licenses a 
problem for my GPL-3 R code? If so, are there recommended ways of resolving 
this?

This post is written from the perspective of an R-package user. I am not an 
R-package developer nor a lawyer. I want to comply with the software licenses 
with the best available understanding about the topic I have.

How did I found the issue: I built a container image from my code, then I ran:

write.csv(installed.packages(fields = "License")[,c(1,10)], 
"Licenses-of-R-packages.csv")

After inspecting the above list I found out that the lme4, central to my code, 
imports the minqa package. The lme4 is licensed under the "GPL-2 | GPL-3 
[expanded from: GPL (≥ 2)]" according to CRAN, and the minqa package under 
"GPL-2". Thus, there might be a license incompatibility. The GPL2 vs GPL3 
incompatibility is stated for example here:

https://www.gnu.org/licenses/gpl-faq.html#v2v3Compatibility

Also if you select both the GPL2 and GPL3 licenses in the following license 
tool, it says they are incompatible:

https://ufal.github.io/public-license-selector/

Here is one of the graphs trying to simplify the license relations. Notice that 
there is no downstream-compatibility arrow from the GPLv2 to the GPLv2+.

https://dwheeler.com/essays/floss-license-slide.html

Here is another figure lacking the compatibility arrow. On the other hand, 
there is no red arrow or cross either. The compatibility graph was obtained 
from the: "Georgia M. Kapitsaki, Nikolaos D. Tselikas, Ioannis E. Foukarakis: 
An insight into license tools for open source software systems. Journal of 
Systems and Software 102: 72-87 (2015)".

https://gkapi.blogspot.com/2016/09/foss-license-compatibilities.html?m=1

The main question is: are there incompatibilities between the upper stream GPL2 
and lower stream "GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]" R packages (minqa 
vs lme4)? If so, how could I deal with the situation as an R-package user 
trying to publish my source code under the GPL3? Or could the issue be solved 
by removing the minqa-based bobyqa optimiser from the lme4 package (a solution 
not directly in my hands)?

Lme4 also suggests the GPL2 numDeriv, is this an issue as well? Furthermore, it 
is notable how the R package installations also install the undirect 
dependencies by default, even if my code works without them, complicating the 
topic further. For example, if I rely on an R package licensed to me with GPL3, 
after the installation my setup (computer or a container image) can be full of 
other and possibly non-complying R packages. One of them being the GPL2 
licensed rbibutils, which becomes installed with the lme4, but the CRAN page of 
the lme4 does not mention this as a direct dependency.

Best regards
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