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

Ruijia Wang rjw@ng@b|o|n|o @end|ng |rom gm@||@com
Fri Aug 20 02:55:15 CEST 2021


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.github using 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.github using gmail.com
> > <mailto: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
> >     <
> 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>
> >     (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>).
> 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
> >
> >      > ).
> >      >
> >      >>
> >      >> * 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 <mailto:Bioc-devel using r-project.org>
> >     mailing list
> >      > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >      >
> >
> >     --
> >     Hervé Pagès
> >
> >     Bioconductor Core Team
> >     hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com>
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>

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