The pryr library is no longer maintained

[frouin]

dear,
As indicated in the title, the pryr library is archived. I work on R v4.5.1
This runing well :

download pryr

download.file("https://cran.r-project.org/src/contrib/Archive/pryr/pryr_0.1.6.tar.gz", destfile = "pryr_0.1.6.tar.gz")

instal pryr

install.packages("pryr_0.1.6.tar.gz", repos = NULL, type = "source")
devtools::install_github('deruncie/MegaLMM', build_opts = c("--no-resave-data", "--no-manual"),force = TRUE,build_vignettes = FALSE)

but for an automatic installation maybe is it possible to implement another lib

[jeanlucj]

MegaLMM cannot be installed on R 4.6: pryr no longer builds [written by Claude at the direction of Jean-Luc Jannink]

(Follow-up to issue #14, "The pryr library is no longer maintained". The
workaround posted there still works on R 4.5 but stops working on R 4.6.)

Summary

pryr was removed from CRAN on 2026-01-30 at its maintainer's request. Issue #14
notes this and works around it by installing pryr_0.1.6.tar.gz from the CRAN
archive. That workaround no longer works on R 4.6: pryr fails to compile,
so install_github("deruncie/MegaLMM") cannot succeed on R 4.6 by any route, and
fails with:

ERROR: dependency 'pryr' is not available for package 'MegaLMM'

MegaLMM barely uses pryr, so this is a two-line fix.

Scope inside MegaLMM: one function, four calls

pryr is used by one function, estimate_memory_initialization_MegaLMM()
in R/helper_functions.R — a diagnostic that prints an estimated memory figure.
It calls require(pryr) inside the function body (line 22) and then uses
object_size() at lines 29, 30, 40 and 44. Nothing is imported from
pryr in NAMESPACE, and the sampler never touches it.

(estimate_memory_posterior() does not use pryr — it is plain arithmetic.)

The only thing that actually forces the dependency is the pryr entry in
DESCRIPTION's Imports:, which R CMD INSTALL checks at install time.

Suggested fix

pryr::object_size has a maintained successor by the same author,
lobstr::obj_size, with the same shared-reference semantics. Three edits:

1. DESCRIPTION — replace pryr with lobstr in Imports:

   MASS,
   tidyr,
-  pryr
+  lobstr

2. R/helper_functions.R, line 22 — drop the runtime attach

 estimate_memory_initialization_MegaLMM = function(MegaLMM_state) {
-  require(pryr)
   print(sprintf("Random effects: %s", ...

3. R/helper_functions.R — qualify the four object_size() calls as
lobstr::obj_size() (lines 29, 30, 40, 44), and wrap the printed total in
as.numeric():

-  print(sprintf("Estimated initialized size: %s Gb", format(signif((estimated_run_variable_size + base_size)/(1024^3), 2))))
+  print(sprintf("Estimated initialized size: %s Gb", format(signif(as.numeric(estimated_run_variable_size + base_size)/(1024^3), 2))))

That last as.numeric() matters: lobstr::obj_size returns a lobstr_bytes
object which format() renders with a unit suffix, so without it the line prints
"Estimated initialized size: 0.10 B Gb".

Zero-dependency alternative

utils::object.size() also works and drops the dependency entirely (just remove
pryr from Imports:). The only difference is that it does not account for
structure shared between components, so it will over-count a nested object like
MegaLMM_state somewhat. For a rough printed estimate that may be acceptable;
lobstr is the closer match to current behavior.

Verification

Tested on R 4.6.1 (2026-06-24), macOS arm64, Apple clang 21, MegaLMM master
2b56997 (2025-10-20), on a real model (201 accessions × 104 trials):

• stock function → FAILS: could not find function "object_size" (after a
  "there is no package called 'pryr'" warning);
• with the edits above → Estimated initialized size: 0.0986 Gb.

Arithmetic in the function (size1 + n * size2, then / 1024^3) was checked
against both lobstr::obj_size and utils::object.size; both support it.

As an interim measure, MegaLMM installs and runs correctly on R 4.6 with pryr
simply deleted from DESCRIPTION's Imports: and no other change — the sampler
is unaffected, and only estimate_memory_initialization_MegaLMM() errors if
called.

Why pryr can no longer be built

R 4.6 removed a set of low-level accessors from the public API. pryr's
src/inspect.cpp uses them, so compilation fails:

inspect.cpp:5:10:  error: use of undeclared identifier 'Rf_findVarInFrame3'
inspect.cpp:23:20: error: use of undeclared identifier 'NAMED'
inspect.cpp:84:34: error: use of undeclared identifier 'FRAME'
inspect.cpp:85:35: error: use of undeclared identifier 'ENCLOS'
inspect.cpp:86:36: error: use of undeclared identifier 'HASHTAB'
inspect.cpp:93:36: error: use of undeclared identifier 'FORMALS'
inspect.cpp:94:33: error: use of undeclared identifier 'BODY'
inspect.cpp:95:33: error: use of undeclared identifier 'CLOENV'
inspect.cpp:101:34: error: use of undeclared identifier 'PRVALUE'
inspect.cpp:109:33: error: use of undeclared identifier 'EXTPTR_PROT'
inspect.cpp:133:7:  error: use of undeclared identifier 'ATTRIB'
inspect.cpp:158:17: error: use of undeclared identifier 'Rf_findVar'
make: *** [inspect.o] Error 1

Defining USE_RINTERNALS does not help: in R 4.6 that guard only covers
MAYBE_SHARED / NO_REFERENCES, not these accessors. Both the CRAN archive
version (0.1.6) and hadley/pryr HEAD (0.1.6.9000) fail identically, and pryr
has been unmaintained since 2018 — so this will not resolve upstream.

[deruncie]

I removed pryr from the dependencies. Try it now