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
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