GO.db for Bioconductor 3.17
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Entering edit mode
@ecbc89ab
Last seen 4 months ago
United States

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
GO.db devel • 1.3k views
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1
Entering edit mode

It seems like there is an issue with a dependent package installation. Could you try reinstalling S4Vectors?

BiocManager::install("S4Vectors", force = TRUE)
library(S4Vectors)

Could you also see what the result is of BiocManager::valid()

ADD REPLY
0
Entering edit mode

I got the same error. The result for package validation is below:

> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

[1] TRUE

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!

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