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

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Mon Dec 19 13:40:44 CET 2022

I can't help much with the segfault

As far as installing through Bioconductor. Until the package installs, builds, and checks cleanly it will not be available.  The fact that it is not listed on the landing page means that it has not yet build since the release on devel and is not available via BiocManager::install

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Jonathon Hill <jhill using byu.edu>
Sent: Friday, December 16, 2022 4:31 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Trying to fix package failing on 3.17


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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