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:
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
installation path not writeable, unable to update packages: XML, boot, class, cluster, codetools,
foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
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:
Did failed also...
installing it using:
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?