ERROR: lazy loading failed for package ‘celldex’

[jess732]

Hi!
I am trying to install the "celldex" package in R, but get a non-zero exit status error. Could you please help me resolve this issue? Thank you very much for your assistance.

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Big Sur 11.3.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Madrid
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base

loaded via a namespace (and not attached):
[1] miniUI_0.1.1.1 compiler_4.4.1
[3] BiocManager_1.30.23 promises_1.3.0
[5] Rcpp_1.0.12 stringr_1.5.1
[7] callr_3.7.6 later_1.3.2
[9] fastmap_1.2.0 mime_0.12
[11] R6_2.5.1 curl_5.2.1
[13] htmlwidgets_1.6.4 desc_1.4.3
[15] profvis_0.3.8 shiny_1.8.1.1
[17] rlang_1.1.4 cachem_1.1.0
[19] stringi_1.8.4 httpuv_1.6.15
[21] fs_1.6.4 pkgload_1.4.0
[23] memoise_2.0.1 cli_3.6.3
[25] magrittr_2.0.3 ps_1.7.6
[27] processx_3.8.4 digest_0.6.36
[29] rstudioapi_0.16.0 xtable_1.8-4
[31] remotes_2.5.0 devtools_2.4.5
[33] lifecycle_1.0.4 vctrs_0.6.5
[35] glue_1.7.0 urlchecker_1.0.1
[37] sessioninfo_1.2.2 pkgbuild_1.4.4
[39] purrr_1.0.2 tools_4.4.1
[41] usethis_2.2.3 ellipsis_0.3.2
[43] htmltools_0.5.8.1

I try to install:
BiocManager::install("celldex")

And I get the following error:

BiocManager::install("celldex")
'getOption("repos")' replaces Bioconductor standard
repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
CRAN: http://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.23), R
4.4.1 (2024-06-14)
Installing package(s) 'celldex'
installing the source package ‘celldex’

trying URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/celldex_1.14.0.tar.gz'
Content type 'application/x-gzip' length 412271 bytes (402 KB)

downloaded 402 KB

• installing source package ‘celldex’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  sh: line 1: 23962 Bus error: 10 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/f4/8xh11j5n3dv30k041x8px0600000gn/T//RtmpIBSskU/file5d95cbe7ba3'

*** caught bus error ***
address 0x100000cfeedfacf, cause 'invalid alignment'

Traceback:
1: register_any_duplicated(set = TRUE)
2: fun(libname, pkgname)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(fun(libname, pkgname), error = identity)
7: runHook(".onLoad", env, package.lib, package)
8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
9: asNamespace(ns)
10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
11: loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, partial = TRUE)
12: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
13: suppressPackageStartupMessages(loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, partial = TRUE))
14: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, compress = compress, set.install.dir = set.install.dir)
15: tools:::makeLazyLoading("celldex", "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-celldex/00new", keep.source = FALSE, keep.parse.data = FALSE, set.install.dir = "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/celldex")
An irrecoverable exception occurred. R is aborting now ...
ERROR: lazy loading failed for package ‘celldex’

• removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/celldex’

The downloaded source packages are in
‘/private/var/folders/f4/8xh11j5n3dv30k041x8px0600000gn/T/RtmpCUlhiE/downloaded_packages’
Old packages: 'Seurat', 'SeuratObject'
Update all/some/none? [a/s/n]:
n
Warning message:
In install.packages(...) :
installation of package ‘celldex’ had non-zero exit status

[LTLA]

I don't know. I've never seen that error before.

This doesn't seem like a problem with celldex, but rather, alabaster.base where register_any_duplicated() is defined. Do you have the same problems with loading alabaster.base?

If so, perhaps try forcibly reinstalling alabaster.base, e.g., BiocManager::install("alabaster.base", force=TRUE).

[jess732]

I have no problems installing BiocManager::install("alabaster.base", force=TRUE), but when I load the library the message "session aborted, the session was terminated" appears.

[LTLA]

Just tried on my own Mac (M2). I don't have any problems with installing or loading the BioC-supplied package.

So, I don't know what's happening in your case. You might check whether other C++-heavy packages from BioC work correctly, to determine whether this is a specific problem with alabaster.base or if it affects other compiled packages. For example, beachmat has lots of C++ code, so you could see if the code below works:

library(beachmat)
example(initializeCpp)

If it does work, it's a problem specific to alabaster.base, but... ¯\_(ツ)_/¯ I don't know why. The relevant code in register_any_duplicated is very simple and I don't see how it would trigger an alignment error.

The only other solution is to build alabaster.base from source, but if you don't already have the relevant toolchains (e.g., XCode), this will be rather painful to set up. Nonetheless you could try cloning the alabaster.base repository and running R CMD INSTALL and see what happens.