Lookup dependencies

[psychemedia]

Several a packages are defined as dependencies in M348 VCE image — M348, nlme, urca, plm, formatR, tseries — and these in turn may have dependencies or imports.

Eg via https://cran-e.com/ we can look up dependencies, imports, suggested/recommended packages etc

• are in core distribution

Pattern is: (required :: imports :: suggests)

• M348 ? ()
• nlme (::graphics, stats, utils*, lattice :: MASS)
• urca (methods :: graphics, stats*, nlme)
• plm (:: MASS, bdsmatrix, collapse≥1.8.9, zoo, nlme, sandwich, lattice, lmtest, maxLik, Rdpack, Formula, stats*:: ...)
• tseries (:: graphics, stats, utils*, quadprog, zoo, quantmod, jsonlite)
• formatR (:: ::)

Imports on imports etc:

• lattice (:: grid, grDevices, graphics, stats, utils*)
• MASS (grDevices, graphics, stats, utils)
• zoo: (stats :: utils, graphics, grDevices, lattice)
• lmtest (stats, zoo:: graphics*)
• Formula (stats*)
• Rdpack (methods :: tools, utils*, rbibutils)
• maxLik (miscTools, methods* :: sandwich, generics)
• sandwich (:: stats, utils, zoo)
• collapse (Rcpp:: ::)
• bdsmatrix (methods*)
• jsonlite (methods*::)
• generics (:: methods*)
• quadprog (::)
• quantmod( xts≥ 0.9-0, zoo, TTR ≥ 0.2, methods :: curl, jsonlite)
• xts (zoo :: methods*)
• TTR (:: xts, zoo, curl)
• miscTools (:: digest)
• digest (:: utils*)
• rbibutils (:: utils, tools)
• curl (:: :: ...)
• Rcpp (:: methods, utils)

TO DO — at least: Rcpp

[psychemedia]

Some of the packages latest version are failing because they expect R 4.4. But we can look to CRAN for old legacy versions, download the src and build from it as a local package; eg https://cran.r-project.org/src/contrib/Archive/MASS/ via a possible lookup recipe here: https://forum.posit.co/t/mass-not-available-for-r-4-3-3/188156/3

* deps::_site/src/contrib/MASS_7.3-61.tar.gz: Needs R >= 4.4.0
ERROR: this R is version 4.3.3, package 'MASS' requires R >= 4.4.0

# Not sure how to cope with compilation error? Try an older src package locally?
ERROR: compilation failed for package 'tseries'

make: *** [/opt/R/4.3.3/lib/R/etc/Makeconf:214: aind.o] Error 1
ERROR: compilation failed for package 'quadprog'

[psychemedia]

Ok - so i can build lots of the above (MASS is okay if we downgrade) but still failing on: tseries, quadprog and curl

In trying to load packages, I can't load:

• library(curl): there is no package called ‘curl’
• library(tseries) Error: Error in Unknown source: package or namespace load failed for ‘TTR’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘curl’
• library(collapse): Error: Unable to download Emscripten filesystem image.See the JavaScript console for further details.
• library(TTR): Error: Error in Unknown source: package ‘TTR’ could not be loaded
• library(quantmod): Error: Error in Unknown source: package ‘TTR’ could not be loaded
• library(quadprog): Requested package quadprog not found in webR binary repo.

I'm also seeing a fail truying to load parallel. This seems to be an R core package, but maybe it's not available in single thread JupyterLite kernel?

Ah, maybe https://joshuaulrich.r-universe.dev/quantmod for quantmod, the 4.3 emscripten package? Nope.

[psychemedia]

Issue with something breaking and trying to load parallel, which is not in core py in webr.

I should maybe have twigged which package might be responsible...

Here's how I tried to track down which package or packages was responsible:

The issue looks like it might be in the collapse package:

The imported function is guarded against by a check on a parallel= argument with default F so a quick hack might just be to comment out that line and rebuild the package locally?