[Bioc-devel] ERROR in the building report of APAlyzer Dev (1.7.3)
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Wed Aug 18 10:36:49 CEST 2021
There's been no activity on Rsubread since Aug 8. You might want to open
an issue on GitHub. It might help.
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:
> 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
> 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.
> 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 (
> > ).
> >> * Error: object 'fout_annot' not found** Backtrace:*
> >> * 1. └─APAlyzer::PASEXP_IPA(...) test_IPA_analysis.R:10:8*
> >> * 2. └─Rsubread::featureCounts(...)** 3.
> > 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
> > 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>
Bioconductor Core Team
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