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
http://bioconductor.org/packages/3.17/bioc/html/sangerseqR.html
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-boun...@r-project.org> on behalf of Jonathon Hill
<jh...@byu.edu>
Sent: Friday, December 16, 2022 4:31 PM
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: [Bioc-devel] Trying to fix package failing on 3.17
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://secure-web.cisco.com/1WQ9FRctS4voq_3uCpC7oa0oRfgVMHTDgY_wy6AUizlaIdzGEyR2TkdbfzpKzzmKJNaJT0PK05WKvnfoQoCBKdxq3gijbHV9QFTNXK8dSIus5-X_8dgaVzMlHCWbL7ki0UVaBOyfOuhNZos2X37vqODVWbDSEsq8C2ov5wyVRAVse1oKF56J2G4mRZJIXo426pHxL1qf52fcAiUa2sfikN6V1gU-paPuC8vA6MsfxE1g2_FhKYtrQPwvUx72vE0bcLS2ipoKlABbcsIszyPFtwntRCkHdG0Uo5aqMxyD3Sf12-pQB5WcuE5C1Ykt4Kt9H/https%3A%2F%2Fcran.r-project.org%2Fdoc%2Fmanuals%2Fr-devel%2FR-admin.html%23Installing-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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