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

[Hervé Pagès]

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

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 
(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).  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
> ).
> 
>>
>> * 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
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