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

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List:       bioc-devel
Subject:    Re: [Bioc-devel]  ERROR in the building report of APAlyzer Dev (1.7.3)
From:       HervÃ© PagÃ¨s <hpages.on.github () gmail ! com>
Date:       2021-08-20 1:14:56
Message-ID: 64370735-cf25-4900-2f3e-11ed32b5ef33 () gmail ! com
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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.github@gmail.com 
> <mailto:hpages.on.github@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@gmail.com <mailto:hpages.on.github@gmail.com>
> > <mailto:hpages.on.github@gmail.com
> <mailto:hpages.on.github@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.github@gmail.com <mailto:hpages.on.github@gmail.com>
> <mailto:hpages.on.github@gmail.com <mailto:hpages.on.github@gmail.com>>
> > 
> 
> -- 
> Hervé Pagès
> 
> Bioconductor Core Team
> hpages.on.github@gmail.com <mailto:hpages.on.github@gmail.com>
> 

-- 
Hervé Pagès

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

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