Message-ID: <428a0fa5-8fac-260c-0c08-1835d3577dc8@gmail.com>
Date: 2022-09-21T02:42:13Z
From: Hervé Pagès
Subject: [Bioc-devel] How to fix the error checked in the development version of miRspongeR
In-Reply-To: <2c4f98df-cb79-21c4-e8cc-af2110cfcf5a@gmail.com>
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, Herv? Pag?s 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 at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Herv? Pag?s
Bioconductor Core Team
hpages.on.github at gmail.com