Thanks, Hervé for your reply.
Now, this error has been fixed (
http://bioconductor.org/checkResults/3.16/bioc-LATEST/miRspongeR/).
According to your suggestion, I have just imported the functions used in
miRspongeR from SPONGE. In addition, I have removed the line
'library(SPONGE)' in vignettes.
On 21/09/2022 07:57, Hervé Pagès wrote:
Just a workaround and not a real solution but maybe try to switch the
order of the clusterProfiler and SPONGE reports?
Oops, I meant "imports", not "reports".
But, again, reducing the huge number of dependencies of both miRspongeR
and SPONGE should be
Let's please keeping this conversation on bioc-devel.
On 20/09/2022 22:36, Zhang Junpeng wrote:
> Thanks for your reply, Hervé.
>
> I have found the cause of this error at
> https://github.com/paul-buerkner/brms/issues/1356 and
> https://github.com/tidyverse/dbplyr/issues/779.
>
> It is Brobding
Looks like there's a nasty clash between dbplyr (CRAN) and the devel
version of clusterProfiler:
> library(clusterProfiler)
> library(dbplyr)
Error in completeSubclasses(classDef2, class1, obj, where) :
trying to get slot "subclasses" from an object of a basic class
("NULL") with no slots
Er
Hi Junpeng,
FWIW the EpiCompare package seems to be failing in exactly the same way:
https://bioconductor.org/checkResults/3.16/bioc-LATEST/EpiCompare/nebbiolo2-install.html
Also I can easily reproduce this on my laptop (Ubuntu 22.04):
> BiocManager::install("miRspongeR")
Bioconductor version
Hi Bioconductor community,
When I build/check the miRspongeR R package (development version), there is
an error as follows. The release version of the miRspongeR R package is OK.
*Error: .onLoad failed in loadNamespace() for 'dbplyr', details:
call: setClass(cl, contains = c(prevClass, "VIRTUAL
