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error installing in R 4.2.2 BC 3.16 #1

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pelacables opened this issue Nov 30, 2023 · 5 comments
Closed

error installing in R 4.2.2 BC 3.16 #1

pelacables opened this issue Nov 30, 2023 · 5 comments

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@pelacables
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Hello,

I'm trying to install the package in R 4.2.2 and Bioconductor 3.16 and I get an error like this:

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
Installing package(s) 'WeberDivechaLCdata'
trying URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WeberDivechaLCdata_1.0.1.tar.gz'
Content type 'application/gzip' length 228679 bytes (223 KB)
==================================================
downloaded 223 KB

* installing *source* package ‘WeberDivechaLCdata’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘WeberDivechaLCdata’
    finding HTML links ... done
    WeberDivechaLCdata                      html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘WeberDivechaLCdata’:
 .onLoad failed in loadNamespace() for 'WeberDivechaLCdata', details:
  call: (function (cond)
  error: error in evaluating the argument 'x' in selecting a method for function 'query': Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/apps/prod/easybuild/sl7.x86_64.foss-2021a/software/BiocLibrary/3.16-foss-2021a-R-4.2.2/site-library/WeberDivechaLCdata’

I'm not a R expert (just a poor sysadmin) and google did not help with this error.
The only bug that sound a bit related is this one https://support.bioconductor.org/p/132864/ but even after setting the PROXY for the ExperimentHub did not help.

could you please help me?

@lcolladotor
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Hm.... from LieberInstitute/recount3#39, maybe your issue is related to Bioconductor/BiocFileCache#50

@lcolladotor
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Note that the fix in Bioconductor/BiocFileCache#50 was implemented only in Bioc release (3.18) and devel (3.19), and you are using an older (and not fixed) version of Bioc (3.16). In short, you might want to upgrade to R 4.3.1 and use Bioc release (3.18).

@pelacables
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ok, so it means that I cannot install the package in 4.2,2 and BC 3,16, right?

@lcolladotor
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It can work in that version of Bioconductor, but you'll have to downgrade a few CRAN package versions. It's simplest to upgrade to BioC 3.18 with R 4.3.1

@pelacables
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Ok, thanks for your answer. I guess I close it now.

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