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Install problem #5

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ybaeus opened this issue Feb 15, 2024 · 4 comments
Open

Install problem #5

ybaeus opened this issue Feb 15, 2024 · 4 comments

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@ybaeus
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ybaeus commented Feb 15, 2024

other attached packages:
[1] TFBSTools_1.40.0 BiocManager_1.30.22 JASPAR2020_0.99.10 igraph_2.0.1.1
[5] GenomicRanges_1.54.1 GenomeInfoDb_1.38.6 IRanges_2.36.0 S4Vectors_0.40.2
[9] BiocGenerics_0.48.1

I faced the error below when i installed JASPAR2022 using BiocManager::install("JASPAR2022").
Do you happen to know what had happened?

Error:
** testing if installed package can be loaded from temporary location
adding rname 'https://jaspar.genereg.net/download/database/JASPAR2022.sqlite'
Warning: download failed
web resource path: ‘https://jaspar.genereg.net/download/database/JASPAR2022.sqlite’
local file path: ‘/home/ybae/.cache/R/BiocFileCache/1fdbc528e4fdc3_JASPAR2022.sqlite’
reason: Not Found (HTTP 404).
Warning: bfcadd() failed; resource removed
rid: BFC7
fpath: ‘https://jaspar.genereg.net/download/database/JASPAR2022.sqlite’
reason: download failed
Warning in value[3L] :

trying to add rname 'https://jaspar.genereg.net/download/database/JASPAR2022.sqlite' produced error:
bfcadd() failed; see warnings()
Error: package or namespace load failed for ‘JASPAR2022’:
.onLoad failed in loadNamespace() for 'JASPAR2022', details:
call: bfcrpath(BiocFileCache(), url)
error: not all 'rnames' found or unique.
Error: loading failed
Execution halted

@da-bar
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da-bar commented Feb 15, 2024

The link to the sqlite file is no longer valid. Please install the latest version of JASPAR2022 either from the Bioconductor development branch or directly from this repo.

@da-bar da-bar closed this as completed Feb 15, 2024
@da-bar da-bar reopened this Feb 15, 2024
@ybaeus
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ybaeus commented Feb 15, 2024

I thought the Biocmagner one was the lastest version.
Could you provide a feasible installation code?

@da-bar
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da-bar commented Feb 16, 2024

You could try like this:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install(version = "devel")
BiocManager::install("JASPAR2022")

In case this doesn't work, then installing from GitHub will certainly work:
if (!requireNamespace("devtools", quietly=TRUE))
install.packages("devtools")
devtools::install_github("da-bar/JASPAR2022")

@ybaeus
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ybaeus commented Feb 24, 2024

Thanks they work !

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