I don't have that information. If the package is not on GitHub then
maybe send an email to its maintainers.
Best,
H.
On 19/08/2021 17:55, Ruijia Wang wrote:
Hi Hervé,
Can share with me the issue page of Rsubread? It seems listed neither on
the Bioconductor page nor on Github. Thanks.
On Wed, Aug 18, 2021 at 4:36 AM Hervé Pagès <hpages.on.git...@gmail.com
<mailto:hpages.on.git...@gmail.com>> wrote:
There's been no activity on Rsubread since Aug 8. You might want to
open
an issue on GitHub. It might help.
H.
On 17/08/2021 16:26, Ruijia Wang wrote:
> 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.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
> <mailto:hpages.on.git...@gmail.com
<mailto:hpages.on.git...@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
<http://bioconductor.org/checkResults/devel/bioc-LATEST/Rsubread/nebbiolo2-buildsrc.html>
>
<http://bioconductor.org/checkResults/devel/bioc-LATEST/Rsubread/nebbiolo2-buildsrc.html <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
<http://git.bioconductor.org>
> <http://git.bioconductor.org <http://git.bioconductor.org>>
> (https://git.bioconductor.org/packages/Rsubread
<https://git.bioconductor.org/packages/Rsubread>
> <https://git.bioconductor.org/packages/Rsubread
<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
<https://bioconductor.org/packages/release/bioc/html/APAlyzer.html>
>
<https://bioconductor.org/packages/release/bioc/html/APAlyzer.html
<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
<http://bioconductor.org/checkResults/devel/bioc-LATEST/APAlyzer/nebbiolo2-checksrc.html>
>
<http://bioconductor.org/checkResults/devel/bioc-LATEST/APAlyzer/nebbiolo2-checksrc.html <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@r-project.org <mailto:Bioc-devel@r-project.org>
<mailto:Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>>
> mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> <https://stat.ethz.ch/mailman/listinfo/bioc-devel
<https://stat.ethz.ch/mailman/listinfo/bioc-devel>>
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
<mailto:hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com>>
>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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