[Bioc-devel] ERROR in the building report of APAlyzer Dev (1.7.3)

[Ruijia Wang]

Thanks so much for your explanation!
I will probably wait for the newer version of Rsubreads to fix it.

On Mon, Aug 16, 2021 at 9:16 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> Hi Ruijia,
>
> I think this is due to recent changes to Rsubread. You can actually see
> the same error here for Rsubread:
>
>
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/Rsubread/nebbiolo2-buildsrc.html
>
> These recent changes to Rsubread did not propagate yet which makes
> things a little hard to reproduce i.e. you can't just use
> BiocManager::install() to get the latest Rsubread. Instead you need to
> install it directly from git.bioconductor.org
> (https://git.bioconductor.org/packages/Rsubread). This is what the build
> system does.
>
> FWIW the reasons the latest changes to Rsubread didn't propagate yet is
> because the package fails to pass 'R CMD build' and also because the
> changes have not been followed by a version bump. Last version bump was
> on July 6 from 2.7.2 to 2.7.3.
>
> Cheers,
> H.
>
>
> On 15/08/2021 17:24, Ruijia Wang wrote:
> > Hi BioC-devel,
> >
> > I am the author of the Bioconductor package APAlyzer (
> > https://bioconductor.org/packages/release/bioc/html/APAlyzer.html).  I
> > current noticed there is an ERROR in the building report of our latest
> dev
> > version  (1.7.3) on the page of Bioconductor (
> >
> http://bioconductor.org/checkResults/devel/bioc-LATEST/APAlyzer/nebbiolo2-checksrc.html
> > ).
> >
> >>
> >> * Error: object 'fout_annot' not found** Backtrace:*
> >>
> >> * 1. └─APAlyzer::PASEXP_IPA(...) test_IPA_analysis.R:10:8*
> >> * 2. └─Rsubread::featureCounts(...)** 3.
> └─base::file.remove(fout_annot)*
> >
> >
> > However, I can not repeat this error using R 4.1 and Bioconductor 3.14 on
> > my end with either *R CMD check* or
> *BiocCheck("APAlyzer_1.7.3.tar.gz").* And
> > I don't recall any of the code updating would trigger the error of
> > *base::file.remove()*. Could you help me to figure out how to fix/bypass
> > this issue in the building report of Bioconductor? Thanks in advance!
> >
> > Best,
> > Ruijia
> >
> >       [[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
> hpages.on.github using gmail.com
>

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