Hi,
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'
Traceback:
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
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages
Any suggestions why I can’t load it?
Thanks,
Jonathon
_____
Jonathon T. Hill, PhD
Associate Professor
Cell Biology and Physiology
Brigham Young University
801-422-8970
Lab: LSB 3035
Office: LSB 3018
Email: jh...@byu.edu<mailto:jh...@byu.edu>
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