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

[Hervé Pagès]

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]]
>      >
>      > _______________________________________________
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>      >
> 
>     -- 
>     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