Search
Question: Error in loading R package topgo
0
gravatar for vjimenez
3.7 years ago by
vjimenez0
Mexico
vjimenez0 wrote:

I am trying to use topGO, but when I want to load this package, I have gotten the following error:

biocLite("topGO")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'topGO'
trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/topGO_2.14.0.tar.gz'
Content type 'application/x-gzip' length 1288615 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb

* installing *source* package ‘topGO’ ...
** R
** data
** inst
** preparing package for lazy loading
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: match.arg(synchronous, c("off", "normal", "full"))
  error: 'arg' must be NULL or a character vector
Error : package ‘GO.db’ could not be loaded
ERROR: lazy loading failed for package ‘topGO’
* removing ‘/home/vjimenez/R/i686-pc-linux-gnu-library/3.0/topGO’

The downloaded source packages are in
    ‘/tmp/RtmpHaAZrQ/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘topGO’ had non-zero exit status

> biocValid()
[1] TRUE
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.12.1

loaded via a namespace (and not attached):
[1] tools_3.0.2

Suggestions?

 

ADD COMMENTlink modified 3.7 years ago by Martin Morgan ♦♦ 22k • written 3.7 years ago by vjimenez0
0
gravatar for Martin Morgan
3.7 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Please see error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db'"

ADD COMMENTlink written 3.7 years ago by Martin Morgan ♦♦ 22k
0
gravatar for vjimenez
3.7 years ago by
vjimenez0
Mexico
vjimenez0 wrote:

Dear Martin:

many thanks for your quick response.  But...

I put:

 install.packages("Downloads/RSQLite_0.11.4.tar.gz", repos=NULL)

and finish with:

* DONE (RSQLite)

Next, I put:
> biocLite("topGO")

and finish with:

* DONE (topGO)

=====

But, when i try:

library(topGO)

Loading required package: graph
Loading required package: Biobase
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 object is masked from ‘package:stats’:

    xtabs

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

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
    lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unlist

Welcome to Bioconductor

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

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: match.arg(synchronous, c("off", "normal", "full"))
  error: 'arg' must be NULL or a character vector
Error: package ‘GO.db’ could not be loaded

====================

I finished in the same place where I started. 

you have any other suggestions? Before, I reinstall R, and I update everything with:
source ("http://bioconductor.org/biocLite.R")
pkgs <- rownames (installed.packages ())
biocLite (pkgs, type = "source")

And I can not get it run

 

ADD COMMENTlink written 3.7 years ago by vjimenez0

biocLite("topGO") would have included an attempt to load the package, and I guess that was successful

** testing if installed package can be loaded
Bioconductor version 3.1 (BiocInstaller 1.17.5), ?biocLite for help

groupGOTerms:     GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (topGO)

or similar. So it is strange that your attempt to load topGO fails. I guess this is because you are using different versions of R, or have different .libPaths() in the two sessions, or you have several versions of the RSQLite package installed.

You indicated that you reinstalled R. Did you re-install the latest version of R, version 3.1.2? Then it should not be necessary to install a special version of RSQLite. Also, try source("http://bioconductor.org/biocLite.R"); biocLite() with no arguments (to update all packages to their current version), and biocValid() to see if there are package incompatibilities.

ADD REPLYlink written 3.7 years ago by Martin Morgan ♦♦ 22k

If you are using R-3.1.2, not only is it not necessary to install an older version of RSQLite, but things will not work if you do. You will need version 1.0.0 (or higher).

ADD REPLYlink written 3.7 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for vjimenez
3.7 years ago by
vjimenez0
Mexico
vjimenez0 wrote:

Dear Martin:

thanks again.

** testing if installed package can be loaded:

biocLite("topGO")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'topGO'

finish with the same error message:

Error : .onLoad failed in loadNamespace() for 'GO.db', details:
call: match.arg(synchronous, c("off", "normal", "full"))
error: 'arg' must be NULL or a character vector
> biocLite("BiocUpgrade")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Warning message:
Bioconductor version 2.13 is the latest available for R version 3.0.0
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
> biocValid()
[1] TRUE


:_(

ADD COMMENTlink modified 3.7 years ago by Martin Morgan ♦♦ 22k • written 3.7 years ago by vjimenez0

biocLite("BiocUpgrade") will not upgrade you to the latest version of Bioconductor. To do that you need to install the latest version of R (3.1.2) and then type source("http://bioconductor.org/biocLite.R") .

ADD REPLYlink written 3.7 years ago by Dan Tenenbaum ♦♦ 8.2k

Do you wish to continue using R 3.0.2 and Bioc 2.13? If so, confirm that the version of RSQLite is correct

packageVersion("RSQLite")      # should be '0.11.4'

If the version of RSQLite is not correct, then install the correct version as you did earlier. Verify that the installed version is now correct. If not, there is no sense in proceeding.

The problem above is with GO.db, so make sure that the version is also correct

packageVersion("GO.db")    # '2.10.1'

If it is not correct, try reinstalling

biocLite("GO.db")

Again, no sense proceeding until this version is correct. Finally, install topGO

biocLite("topGO")

If at any stage you do not have success, then please post the _entire_ command that you entered and the output generated.

ADD REPLYlink written 3.7 years ago by Martin Morgan ♦♦ 22k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 413 users visited in the last hour