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Question: Problems with the correct installation of GOseq
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gravatar for thijmen.breeschoten
3 months ago by
thijmen.breeschoten0 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 3 months ago by stephenhawking6160 • written 3 months ago by thijmen.breeschoten0
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 3 months ago by Lluís R330

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 3 months ago by thijmen.breeschoten0

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 3 months ago by thijmen.breeschoten0
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