[Bioc-devel] EXTERNAL: Fwd: PREDA problems reported in the Multiple platform build/check report for BioC 3.7

[Francesco Ferrari]

Dear Lori,

I already foxed the issue in the devel branch which now gives a clean check:
 https://bioconductor.org/checkResults/3.8/bioc-LATEST/

The problema was due to a CRAN  dependency no more available since July 20, 2018.

Would you recommend fixing the same issue also in the current release branch?
Or shall I leave it unchanged for consistency?

All the best
Francesco





> On 6 Aug 2018, at 20:33, Shepherd, Lori <Lori.Shepherd using RoswellPark.org> wrote:
> 
> You can wait a little longer if you like.  It might also be helpful to reach out to the samr maintainers to see if they have any intention of bringing it back onto CRAN.  I would not recommend waiting too long, as the package will need to be fixed before the next release to avoid deprecation in release Bioc 3.8. While there is no official release date set - it is generally in October.
> 
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> From: Bioc-devel <bioc-devel-bounces using r-project.org <mailto:bioc-devel-bounces using r-project.org>> on behalf of Francesco Ferrari <francesco.ferrari using ifom.eu <mailto:francesco.ferrari using ifom.eu>>
> Sent: Monday, August 6, 2018 12:18:43 PM
> To: bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>
> Subject: EXTERNAL: [Bioc-devel] Fwd: PREDA problems reported in the Multiple platform build/check report for BioC 3.7
>  
> Looks like a CRAN package is no more available, and this is triggering a problem with a “suggested” dependency
> 
> * checking package dependencies ... ERROR
> Package suggested but not available: ‘samr’
> 
> which indeed has been removed from CRAN on July 20:
> 
> https://cran.r-project.org/web/packages/samr/index.html <https://cran.r-project.org/web/packages/samr/index.html> <https://cran.r-project.org/web/packages/samr/index.html <https://cran.r-project.org/web/packages/samr/index.html>>
> 
> 
> It may be a temporary issue (while the develpers fix it) or a more long term one.
> 
> Should I remove the dependency right away or wait a bit longer?
> 
> 
> 
> 
> 
> 
> 
> 
> > Begin forwarded message:
> > 
> > From: BBS-noreply using bioconductor.org <mailto:BBS-noreply using bioconductor.org>
> > Subject: PREDA problems reported in the Multiple platform build/check report for BioC 3.7
> > Date: 6 Aug 2018 18:14:02 CEST
> > To: francesco.ferrari using ifom.eu <mailto:francesco.ferrari using ifom.eu>
> > 
> > [This is an automatically generated email. Please don't reply.]
> > 
> > Hi PREDA maintainer,
> > 
> > According to the Multiple platform build/check report for BioC 3.7,
> > the PREDA package has the following problem(s):
> > 
> >  o ERROR for 'R CMD check' on malbec2. See the details here:
> >      https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/PREDA/malbec2-checksrc.html <https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/PREDA/malbec2-checksrc.html>
> > 
> > Please take the time to address this by committing and pushing
> > changes to your package at git.bioconductor.org <http://git.bioconductor.org/>
> > 
> > Notes:
> > 
> >  * This was the status of your package at the time this email was sent to you.
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> >    could see something different when you visit the URL(s) above, especially if
> >    you do so several days after you received this email.
> > 
> >  * It is possible that the problems reported in this report are false positives,
> >    either because another package (from CRAN or Bioconductor) breaks your
> >    package (if yours depends on it) or because of a Build System problem.
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> > 
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