Re: [Bioc-devel] seqArchR error on build systems

[Hervé Pagès]

Hi Sarvesh,

It looks like reticulate somehow was using the wrong Python instance on 
nebbiolo2 and lconway, as reported by py_config().


We're now setting RETICULATE_PYTHON on those machines to make sure that 
reticulate will use the correct Python. This change was made after the 
builds started today so it won't be reflected on tomorrow's report. But 
it should be reflected on Thursday's report.


We'll do the same on the other build machines soon.

Best,

H.

On 25/10/2022 08:53, Sarvesh Nikumbh wrote:

Hi Bioc-team,

seqArchR was building fine, without any errors last week, but I am seeing
an error again. This time it is due to the Python module 'sklearn' not
available and one another error. The sklearn-related error occurs on
nebbiolo2 and Iconway, while palomino4 shows a different error.

Maybe something changed on the build systems? Because these system
requirements were available before*.*

Thanks and best,
   Sarvesh


--
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Package dependencies error during BiocCheck

[Sarvesh Nikumbh]

Hi Marcel,

Thanks for the reply.

Is there a way to opt for this solution on the bioc new pkg build systems?

If not, then, I guess, I will have to wait until it goes away for my bioc
submission to be reviewed further?

Thanks and best,
  Sarvesh


On Tue, 25 Oct 2022, 18:14 Marcel Ramos, 
wrote:

> Hi Sarvesh,
>
> The error has something to do with an interaction between internal base
> R code
> and checking for dependencies in BiocCheck with `loadNamespace`.
> Either way, this check in BiocCheck is redundant with R CMD check.
> It will soon get removed but for now, you can disable it by running:
>
> BiocCheck("./seqArchRplus", `no-check-dependencies` = TRUE)
>
> Best,
>
> Marcel
>
>
> On 10/25/22 12:27 PM, Sarvesh Nikumbh wrote:
> > Hi all,
> >
> > I am trying to resolve an issue with dependencies of my package which is
> > under review at the moment (Issue 2790
> > , latest
> report
> > <
> http://bioconductor.org/spb_reports/seqArchRplus_buildreport_20221025084934.html
> >).
> > I was wondering if somebody else also encountered this issue (see details
> > below), and were successful resolving it. Any help in this regard would
> be
> > greatly appreciated.
> >
> > *The issue:*
> > Running BiocCheck throws the following error:
> >
> > 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
> >
> > which going by info at
> > tidyverse/dbplyr#779  is
> > caused by Brobdingnag, and
> > resolved with version 1.2-9, which is now also available on CRAN (see
> here
> > ).
> >
> > I saw this error earlier on my debian machine only using bioc-devel.
> Here,
> > I could resolve this by re-installing Matrix, dbplyr and Brobdingnag.
> >
> > On bioc-side, the error can be seen on Ubuntu (latest report
> > <
> http://bioconductor.org/spb_reports/seqArchRplus_buildreport_20221025084934.html
> >).
> > Maybe, it would occur on other OSs as well, but that stage is not
> reached.
> > Thanks to Lori and Jennifer from bioc-team, the same re-installation
> > solution was attempted, but this did not resolve it there.
> >
> > Since I do not have access to a machine running Ubuntu around, I have set
> > up GHA. There, interestingly, the same error is encountered on macOS and
> > Windows, but not on Ubuntu -- details here
> > <
> https://github.com/snikumbh/seqArchRplus/actions/runs/3322212068/jobs/5490915503
> >
> > .
> >
> >
> > Any leads?
> >
> > Thanks in advance.
>
> This email message may contain legally privileged and/or...{{dropped:4}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Package dependencies error during BiocCheck

[Marcel Ramos]

Hi Sarvesh,

The error has something to do with an interaction between internal base 
R code
and checking for dependencies in BiocCheck with `loadNamespace`.
Either way, this check in BiocCheck is redundant with R CMD check.
It will soon get removed but for now, you can disable it by running:

BiocCheck("./seqArchRplus", `no-check-dependencies` = TRUE)

Best,

Marcel


On 10/25/22 12:27 PM, Sarvesh Nikumbh wrote:
> Hi all,
>
> I am trying to resolve an issue with dependencies of my package which is
> under review at the moment (Issue 2790
> , latest report
> ).
> I was wondering if somebody else also encountered this issue (see details
> below), and were successful resolving it. Any help in this regard would be
> greatly appreciated.
>
> *The issue:*
> Running BiocCheck throws the following error:
>
> 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
>
> which going by info at
> tidyverse/dbplyr#779  is
> caused by Brobdingnag, and
> resolved with version 1.2-9, which is now also available on CRAN (see here
> ).
>
> I saw this error earlier on my debian machine only using bioc-devel. Here,
> I could resolve this by re-installing Matrix, dbplyr and Brobdingnag.
>
> On bioc-side, the error can be seen on Ubuntu (latest report
> ).
> Maybe, it would occur on other OSs as well, but that stage is not reached.
> Thanks to Lori and Jennifer from bioc-team, the same re-installation
> solution was attempted, but this did not resolve it there.
>
> Since I do not have access to a machine running Ubuntu around, I have set
> up GHA. There, interestingly, the same error is encountered on macOS and
> Windows, but not on Ubuntu -- details here
> 
> .
>
>
> Any leads?
>
> Thanks in advance.

This email message may contain legally privileged and/or...{{dropped:4}}

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[Bioc-devel] Package dependencies error during BiocCheck

[Sarvesh Nikumbh]

Hi all,

I am trying to resolve an issue with dependencies of my package which is
under review at the moment (Issue 2790
, latest report
).
I was wondering if somebody else also encountered this issue (see details
below), and were successful resolving it. Any help in this regard would be
greatly appreciated.

*The issue:*
Running BiocCheck throws the following error:

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

which going by info at
tidyverse/dbplyr#779  is
caused by Brobdingnag , and
resolved with version 1.2-9, which is now also available on CRAN (see here
).

I saw this error earlier on my debian machine only using bioc-devel. Here,
I could resolve this by re-installing Matrix, dbplyr and Brobdingnag.

On bioc-side, the error can be seen on Ubuntu (latest report
).
Maybe, it would occur on other OSs as well, but that stage is not reached.
Thanks to Lori and Jennifer from bioc-team, the same re-installation
solution was attempted, but this did not resolve it there.

Since I do not have access to a machine running Ubuntu around, I have set
up GHA. There, interestingly, the same error is encountered on macOS and
Windows, but not on Ubuntu -- details here

.


Any leads?

Thanks in advance.
-- 

thanks!
-Sarvesh

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[Bioc-devel] seqArchR error on build systems

[Sarvesh Nikumbh]

Hi Bioc-team,

seqArchR was building fine, without any errors last week, but I am seeing
an error again. This time it is due to the Python module 'sklearn' not
available and one another error. The sklearn-related error occurs on
nebbiolo2 and Iconway, while palomino4 shows a different error.

Maybe something changed on the build systems? Because these system
requirements were available before*.*

Thanks and best,
  Sarvesh

-- 

thanks!
-Sarvesh


Q: Why is this email five sentences or less?
A: http://five.sentenc.es

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