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

[Hervé Pagès]

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
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