Exporting getDb

[yulab-smu]

Exporting getDb

[GuangchuangYu]

you are using devel branch of GOSemSim, then you need to use corresponding branch of DOSE and ReactomePA.

devtools::install_bioc(c("DOSE", "ReactomePA"))

[LiNk-NY]

I am using bioc-devel. You are missing an @export tag on getDb.

[GuangchuangYu]

it was move to ReactomePA, see https://github.com/GuangchuangYu/ReactomePA/blob/master/R/utilities.R

[LiNk-NY]

Yes, I see that. You need to export this function from ReactomePA.

BiocInstaller::biocLite("ReactomePA") returns an error:

Error : object ‘getDb’ is not exported by 'namespace:GOSemSim'
ERROR: lazy loading failed for package ‘ReactomePA’

We know it's not exported from GOSemSim because it was moved to ReactomePA. It can't be found because it's not exported in the ReactomePA NAMESPACE.

[GuangchuangYu]

it's not used elsewhere. Why I need to export it ?

[LiNk-NY]

Hi @GuangchuangYu,
If it is meant to be internal then you don't need to document it. What I usually do is add a period ('.') in front of the function so that it isn't picked up as an object that should be documented and exported by the checks.
This will resolve the error that appears when installing.

[GuangchuangYu]

the issue is due to mixing installation of release and devel branch and not related to the documentation and function name.

[LiNk-NY]

The version number has not been updated and thus the package in the Bioc servers is not being re-build properly with the new changes please bump your version so that the package can be installed via BiocInstaller::biocLite("ReactomePA")

See #7

Regards,
Marcel

[GuangchuangYu]

by default, BiocInstaller::biocLite("ReactomePA") will always install the release version.

In release branch, ReactomePA is still import getDb from GOSemSim.

Here, we are talking about the devel branch. You need to install it by:

library(BiocInstaller)
useDevel()
biocLite("ReactomePA")

Referring to #7, you need to wait 2-3 days for Bioconductor to update tarball or use devtools::install_bioc() to install it from svn repository as I also mentioned in https://github.com/ManuelGoepferich/LINC/issues/1#issuecomment-237126811.

[LiNk-NY]

Yes, I know that. I'm using and have been using the devel version of Bioconductor for a while now. Even using the devel branch, that error appears which indicates that your changes haven't been propagated due to the version bump issue.
Thanks for updating that.