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>> 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.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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