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

[Hervé Pagès]

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 using gmail.com 
> <mailto: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>
>      > <mailto: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>
>      >   
>       <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]]
>      >      >
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>      >      >
>      >
>      >     --
>      >     Hervé Pagès
>      >
>      >     Bioconductor Core Team
>      > hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com>
>     <mailto:hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com>>
>      >
> 
>     -- 
>     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