Entering edit mode
Hi,
I'm hoping to get a package ready for the 3.17 Bioconductor release but I am unable to get a functional GO.db package for the devel version
> BiocManager::install(version='devel')
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.19), R Under development (unstable)
(2023-01-18 r83642)
>
> BiocManager::install("GO.db")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.19), R Under development (unstable)
(2023-01-18 r83642)
Installing package(s) 'GO.db'
Warning: unable to access index for repository https://cran.rstudio.com/bin/macosx/contrib/4.3:
cannot open URL 'https://cran.rstudio.com/bin/macosx/contrib/4.3/PACKAGES'
installing the source package ‘GO.db’
trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GO.db_3.16.0.tar.gz'
Content type 'application/x-gzip' length 29540685 bytes (28.2 MB)
==================================================
downloaded 28.2 MB
* installing *source* package ‘GO.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 16291 Segmentation fault: 11 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/nf/3cb4kv693xjbfhh7vfqnn3ww0000gp/T//RtmpQWgXF9/file3f9ab892723'
*** 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 ...
ERROR: lazy loading failed for package ‘GO.db’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library/GO.db’
The downloaded source packages are in
‘/private/var/folders/nf/3cb4kv693xjbfhh7vfqnn3ww0000gp/T/RtmpQSZumg/downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘GO.db’ had non-zero exit status
>
> sessionInfo( )
R Under development (unstable) (2023-01-18 r83642)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
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: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biobase_2.59.0 graph_1.77.1 BiocGenerics_0.45.0
loaded via a namespace (and not attached):
[1] digest_0.6.31 fastmap_1.1.0 xfun_0.37 knitr_1.42
[5] htmltools_0.5.4 rmarkdown_2.20 stats4_4.3.0 cli_3.6.0
[9] compiler_4.3.0 rstudioapi_0.14 tools_4.3.0 evaluate_0.20
[13] yaml_2.3.7 BiocManager_1.30.19 rlang_1.0.6
It seems like there is an issue with a dependent package installation. Could you try reinstalling S4Vectors?
Could you also see what the result is of
BiocManager::valid()
I got the same error. The result for package validation is below:
after a bit more searching, I think this is an issue with failure of r-devel on high-sierra right now. got it working just fine on the docker.
Thank you!