[Bioc-devel] How to fix the error checked in the development version of miRspongeR

[Hervé Pagès]

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 Brobdingnag which caused the bug which is a dependency from 
> bridgsamplin. But, I have no way to solve this error now. It seems 
> that several other packages have also the same error.

Just a workaround and not a real solution but maybe try to switch the 
order of the clusterProfiler and SPONGE reports?

Best,

H.

>
> Regards,
> Junpeng
>
> Hervé Pagès <hpages.on.github using gmail.com> 于2022年9月21日周三 10:42写道：
>
>     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
>     Error: package or namespace load failed for ‘dbplyr’:
>       .onLoad failed in loadNamespace() for 'dbplyr', details:
>        call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where =
>     where)
>        error: error in contained classes ("character") for class “ident”;
>     class definition removed from ‘dbplyr’
>
>     This is on any platform with Bioc-devel and the latest version of
>     each
>     package:
>
>        > packageVersion("clusterProfiler")
>        [1] ‘4.5.2’
>        > packageVersion("dbplyr")
>        [1] ‘2.2.1’
>
>     Note that you need to load the two packages in this order to get this
>     error. Loading them in the opposite order works fine.
>
>     This seems to break miRspongeR thru a series of events that
>     involve the
>     imports made by the SPONGE package:  miRspongeR imports
>     clusterProfiler
>     and SPONGE, in that order, and SPONGE itself imports dbplyr via
>     tidyverse.
>
>     This is something you'll have to discuss with the clusterProfiler
>     and/or
>     dbplyr maintainers.
>
>     Finally note that, when miRspongeR is loaded, sessionInfo() reports
>     about 200 packages loaded via a namespace! This is obviously a very
>     fragile situation. Reducing that number would help make the
>     package less
>     vulnerable to these sorts of clash. Many of those "loaded via a
>     namespace" packages are actually a consequence of SPONGE itself
>     importing many many things (it imports the full tidyverse!), so
>     there's
>     probably some room for improvement on that side too.
>
>     Best,
>
>     H.
>
>
>     On 20/09/2022 13:32, Hervé Pagès wrote:
>     > 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 3.16 (BiocManager 1.30.18), R 4.2.0 Patched
>     > (2022-05-04
>     >   r82318)
>     > Installing package(s) 'miRspongeR'
>     > trying URL
>     >
>     'https://bioconductor.org/packages/3.16/bioc/src/contrib/miRspongeR_2.1.0.tar.gz'
>
>     >
>     > Content type 'application/x-gzip' length 661557 bytes (646 KB)
>     > ==================================================
>     > downloaded 646 KB
>     >
>     > * installing *source* package ‘miRspongeR’ ...
>     > ** using staged installation
>     > ** libs
>     > /usr/bin/gcc -I"/home/hpages/R/R-4.2.r82318/include" -DNDEBUG
>     > `/home/hpages/R/R-4.2.r82318/bin/Rscript -e "Rcpp:::CxxFlags()"`
>     > -I/usr/local/include   -fpic  -O3 -c complex.c -o complex.o
>     > /usr/bin/gcc -I"/home/hpages/R/R-4.2.r82318/include" -DNDEBUG
>     > `/home/hpages/R/R-4.2.r82318/bin/Rscript -e "Rcpp:::CxxFlags()"`
>     > -I/usr/local/include   -fpic  -O3 -c registerDynamicSymbol.c -o
>     > registerDynamicSymbol.o
>     > /usr/bin/gcc -shared -L/home/hpages/R/R-4.2.r82318/lib
>     > -L/usr/local/lib -o miRspongeR.so complex.o registerDynamicSymbol.o
>     > -L/home/hpages/R/R-4.2.r82318/lib -lR
>     > installing to
>     >
>     /home/hpages/R/R-4.2.r82318/library/00LOCK-miRspongeR/00new/miRspongeR/libs
>     > ** R
>     > ** inst
>     > ** byte-compile and prepare package for lazy loading
>     > Error in completeSubclasses(classDef2, class1, obj, where) :
>     >   trying to get slot "subclasses" from an object of a basic class
>     > ("NULL") with no slots
>     > Error: .onLoad failed in loadNamespace() for 'dbplyr', details:
>     >   call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where =
>     where)
>     >   error: error in contained classes ("character") for class
>     “ident”;
>     > class definition removed from ‘dbplyr’
>     > Execution halted
>     > ERROR: lazy loading failed for package ‘miRspongeR’
>     > * removing ‘/home/hpages/R/R-4.2.r82318/library/miRspongeR’
>     >
>     > The downloaded source packages are in
>     >     ‘/tmp/RtmpzFvmcs/downloaded_packages’
>     > Updating HTML index of packages in '.Library'
>     > Making 'packages.html' ... done
>     >
>     > Let me take a closer look.
>     >
>     > H.
>     >
>     > On 20/09/2022 03:50, Zhang Junpeng wrote:
>     >> 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"), where
>     = where)
>     >>    error: error in contained classes ("character") for class
>     “ident”;
>     >> class
>     >> definition removed from ‘dbplyr’
>     >> Execution halted*
>     >>
>     >> How can I fix this error? The details of error here:
>     >>
>     https://master.bioconductor.org/checkResults/3.16/bioc-LATEST/miRspongeR/nebbiolo2-buildsrc.html
>
>     >>
>     >>
>     >> Thanks in advance
>     >> Junpeng
>     >>
>     >>     [[alternative HTML version deleted]]
>     >>
>     >> _______________________________________________
>     >> Bioc-devel using r-project.org mailing list
>     >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>     >
>     -- 
>     Hervé Pagès
>
>     Bioconductor Core Team
>     hpages.on.github using gmail.com
>
-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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