Search
Question: Problems with the correct installation of GOseq
0
gravatar for TB18
6 months ago by
TB180
TB180 wrote:

Dear community,

I have great difficulty in installing the package 'GOseq', I searched google for similar issues but all seem not applicable for me or result in the same error.

At first I tried installing:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("goseq")

This results in the following error:

Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: NULL
  error: C stack usage  7969392 is too close to the limit
ERROR: lazy loading failed for package ‘goseq’
* removing ‘/home/biosys5/R/x86_64-pc-linux-gnu-library/3.4/goseq’

The downloaded source packages are in
    ‘/tmp/Rtmp8pCoGD/downloaded_packages’
installation path not writeable, unable to update packages: XML, boot, class, cluster, codetools,
  foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘goseq’ had non-zero exit status

So there seems something wrong with the stack size. So I set the stack size to unlimited in my terminal using:

>ulimit -s unlimited

I checked this with ulimit -a and it all seemed fine.

Running the command again, however, results in the same error...

Installing it via:

source("https://bioconductor.org/biocLite.R")
biocLite("goseq")

Did failed also...

And finally:

installing it using:

biocLite(c("AnnotationDbi", "GO.db"), type="source")
source('http://bioconductor.org/biocLite.R')
install.packages("goseq", repos="http://bioconductor.org/packages/2.11/bioc")
library(goseq)

Results in the installation of GOseq but running the program (with the Trinity pipeline) constantly gives me the error:

Full error message:

Error: package or namespace load failed for ‘GO.db’: .onLoad failed in loadNamespace() for 'GO.db', details: call: NULL error: evaluation nested too deeply: infinite recursion / options(expressions=)? Execution halted

I received the advice to reinstall GOseq because there is probably something wrong with the installation of the program...

Does anyone have a sollution?

 

go
ADD COMMENTlink modified 6 months ago by stephenhawking6160 • written 6 months ago by TB180
The first error says: "installation path not writeable, unable to update package", you seem to need to update the packages to installl GOseq. Which version of R and Bioconductor are you using? Are they up to date?
ADD REPLYlink written 6 months ago by Lluís R370

Ah! Forgot to mention. Yes, I updated the versions I'm using:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help

and R:

version.string R version 3.4.3 (2017-11-30)

ADD REPLYlink written 6 months ago by TB180

Perhaps worthwhile to mention. If I just try to load GO.db I get the following error message (related to the issue above):

> library(GO.db)
Error: package or namespace load failed for ‘GO.db’:
 .onLoad failed in loadNamespace() for 'GO.db', details:
  call: NULL
  error: C stack usage  7970192 is too close to the limit

ADD REPLYlink written 6 months ago by TB180
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: 317 users visited in the last hour