Re: [Bioc-devel] How to fix the error checked in the development version of miRspongeR
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. If possible, I will fork a part of functions in SPONGE instead of importing it. Regards, Junpeng. Hervé Pagès 于2022年9月24日周六 03:00写道： > 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 a priority. Something that you might want to > discuss/coordinate with the SPONGE folks. > > Best, > > H. > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] How to fix the error checked in the development version of miRspongeR
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 a priority. Something that you might want to discuss/coordinate with the SPONGE folks. Best, H. -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] How to fix the error checked in the development version of miRspongeR
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 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’
> >
Re: [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, 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@r-project.org mailing list
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--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] How to fix the error checked in the development version of miRspongeR
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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] How to fix the error checked in the development version of miRspongeR
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]]
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