[Bioc-devel] How to fix the error checked in the development version of miRspongeR
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
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Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com