GO.db for Bioconductor 3.17
0
0
Entering edit mode
@ecbc89ab
Last seen 3 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
ADD COMMENT
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!

ADD REPLY

Login before adding your answer.

Traffic: 1016 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6