Question: GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
1
gravatar for Jens Preussner
16 months ago by
Germany
Jens Preussner30 wrote:

Hi all,

I'm trying to install GO.db on Mac OS X with R3.5.0 and Bioconductor 3.7.0:

> library(AnnotationDbi)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,
    parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans,
    rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid
> biocLite("GO.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘GO.db’
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GO.db_3.6.0.tar.gz'
Content type 'application/x-gzip' length 31763273 bytes (30.3 MB)
==================================================
downloaded 30.3 MB

* installing *source* package ‘GO.db’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : package ‘AnnotationDbi’ required by ‘GO.db’ could not be found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/jpreuss/Library/R/3.5/library/GO.db’

The downloaded source packages are in
    ‘/private/var/folders/1v/3by9kjrd6ljd1jz3d04x8dqm7cdgs6/T/RtmpEmgcl1/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status

I tried specifying lib.loc and installing via R CMD INSTALL, but both failed with the same error. Also installing other annotation packages, like BSgenome.Mmusculus.UCSC.mm10 fail for me. There is no traceback() available.

Any ideas? Many thanks, Jens

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] AnnotationDbi_1.42.1 IRanges_2.14.10      S4Vectors_0.18.2     Biobase_2.40.0       BiocGenerics_0.26.0  BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17   digest_0.6.15  DBI_1.0.0      RSQLite_2.1.1  blob_1.1.1     tools_3.5.0    bit64_0.9-7    bit_1.1-14     compiler_3.5.0 memoise_1.1.0
ADD COMMENTlink modified 16 months ago by Martin Morgan ♦♦ 23k • written 16 months ago by Jens Preussner30
Answer: GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
0
gravatar for Martin Morgan
16 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Did you try to install the missing dependency (this shouldn't usually be necessary, but that is what R says is the problem...)?

biocLite("AnnotationDbi")  # if this is successful, then...
biocLite("GO.db")

(Usually one could install multiple packages via biocLite(c("AnnotationDbi", "GO.db")), but since you're having trouble let's do things one step at a time...)

ADD COMMENTlink written 16 months ago by Martin Morgan ♦♦ 23k

Thanks for your reply. AnnotationDbi installation is successful, but GO.db fails afterwards with the error message seen above.

ADD REPLYlink modified 16 months ago • written 16 months ago by Jens Preussner30
1

Can you investigate where AnnotationDbi is installed, e.g., looking at something like

sapply(.libPaths(), function(elt) "AnnotationDbi" %in% dir(elt))

I don't really know where this will lead, but I would guess that you have two or more .libPaths(), that AnnotationDbi is in a path different from the location (probably the first entry in .libPaths()) where GO.db is being installed.

Another approach might first remove AnnotationDbi (via remove.packages("AnnotationDbi"), repeated until R says there is no package to remove) and then (in a new session) install it again...

A different tack might be to try to install GO.db without testing that it can be loaded, and one installed in a new session try to load -- exploring the idea that the libPaths() at installation are different from the run-time installation. This could be done at the command line with

R CMD INSTALL --no-test-load GO.db_...

or from within R with

biocLite("GO.db", INSTALL_opts = "--no-test-load")
ADD REPLYlink written 16 months ago by Martin Morgan ♦♦ 23k
1

Thats great! Thank you for your time and effort. R CMD INSTALL --no-test-load GO.db_... did the trick! Who knows why the .libPaths() are different between installation and run time, but it worked now. Thanks again for your help! Highly appreciated!

ADD REPLYlink modified 16 months ago • written 16 months ago by Jens Preussner30

Glad that worked, can you provide me with the output of .libPaths() and sapply(.libPaths(), function(elt) "AnnotationDbi" %in% dir(elt)) ? it will help to debug this further.

ADD REPLYlink modified 16 months ago • written 16 months ago by Martin Morgan ♦♦ 23k
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