[Bioc-devel] Trying to fix package failing on 3.17

Jonathon Hill jh||| @end|ng |rom byu@edu
Fri Dec 16 22:31:35 CET 2022


I received a notice that my package, sangerseqR, is failing during the nightly build process for the devel branch (3.17) of bioconductor.

I do not see an error when I use the package in the current build, so it is something specific to the new build.

I have been trying to recreate the error. I downloaded and installed R 4.3 and installed the Bioconductor devel packages. However, when I try to build my package locally, I get the following error:

==> R CMD INSTALL --preclean --no-multiarch --with-keep.source sangerseqR

* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘sangerseqR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return && !quietly)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
 9: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,     .libPaths()))
10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
11: .getRequiredPackages2(pkgInfo, quietly, lib.loc, useImports)
12: .getRequiredPackages(quietly = TRUE)
13: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
14: suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))
An irrecoverable exception occurred. R is aborting now ...
sh: line 1:  6601 Segmentation fault: 11  R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/1w/yqm9vhw952s4dbb2g9vtr_6r0000gp/T//RtmpRo37lg/file19c36696d396'
ERROR: lazy loading failed for package ‘sangerseqR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library/sangerseqR’

Exited with status 1.

Furthermore, when I try to install my package through bioconductor, I get:

Warning message:
package ‘sangerseqR’ is not available for Bioconductor version '3.17'

A version of this package for your version of R might be available elsewhere,
see the ideas at

Any suggestions why I can’t load it?




Jonathon T. Hill, PhD
Associate Professor
Cell Biology and Physiology
Brigham Young University
Lab: LSB 3035
Office: LSB 3018
Email: jhill using byu.edu<mailto:jhill using byu.edu>

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