da-bar / JASPAR2022

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Issue on JASPAR2022 Installation #4

Closed ScienceComputing closed 7 months ago

ScienceComputing commented 7 months ago

Hi developer,

When typing BiocManager::install("JASPAR2022"), the following error message pops up. Could you advise how to address it? I look forward to learning your insights. Many thanks in advance.

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Installing package(s) 'JASPAR2022'
installing the source package ‘JASPAR2022’

trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/JASPAR2022_0.99.7.tar.gz'
Content type 'application/x-gzip' length 270129 bytes (263 KB)
==================================================
downloaded 263 KB

* installing *source* package ‘JASPAR2022’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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: ‘/Users/anniliu/Library/Caches/org.R-project.R/R/BiocFileCache/14294722e0ee_JASPAR2022.sqlite’
  reason: SSL peer certificate or SSH remote key was not OK: [jaspar.genereg.net] SSL: no alternative certificate subject name matches target host name 'jaspar.genereg.net'
Warning: bfcadd() failed; resource removed
  rid: BFC4
  fpath: ‘https://jaspar.genereg.net/download/database/JASPAR2022.sqlite’
  reason: download failed
Warning in value[[3L]](cond) :

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
ERROR: loading failed
* removing ‘/Users/oen/Library/R/x86_64/4.3/library/JASPAR2022’

The downloaded source packages are in
    ‘/private/var/folders/s1/6460_yvs6ggdv14vc1dsk_r40000gn/T/RtmpZnlnza/downloaded_packages’
Old packages: 'AnnotationDbi', 'AnnotationHub', 'Biobase', 'BiocFileCache', 'BiocGenerics', 'BiocIO', 'BiocParallel', 'BiocVersion', 'biomaRt', 'Biostrings', 'breastCancerMAINZ', 'clusterProfiler', 'DelayedArray', 'DESeq2', 'DOSE', 'edgeR', 'enrichplot', 'fgsea', 'geneLenDataBase',
  'GenomeInfoDb', 'GenomeInfoDbData', 'GenomicAlignments', 'GenomicFeatures', 'GenomicRanges', 'ggtree', 'GO.db', 'GOSemSim', 'goseq', 'graph', 'graphite', 'interactiveDisplayBase', 'IRanges', 'KEGGREST', 'limma', 'MatrixGenerics', 'MeSHDbi', 'meshes', 'org.Hs.eg.db', 'org.Mm.eg.db', 'qvalue',
  'reactome.db', 'ReactomePA', 'Rhtslib', 'Rsamtools', 'rtracklayer', 'S4Arrays', 'S4Vectors', 'seqLogo', 'SummarizedExperiment', 'treeio', 'viridis', 'XVector', 'zlibbioc'
Update all/some/none? [a/s/n]: 
n
Warning message:
In install.packages(...) :
  installation of package ‘JASPAR2022’ had non-zero exit status
da-bar commented 7 months ago

Hi @ScienceComputing The error was caused due to a broken link, which has now being fixed. Please use the development branch of Bioconductor or install it directly from this GitHub page to install the package. Sorry for the inconvenience.

ScienceComputing commented 7 months ago

Hi @ScienceComputing The error was caused due to a broken link, which has now being fixed. Please use the development branch of Bioconductor or install it directly from this GitHub page to install the package. Sorry for the inconvenience.

Thank you so so much for your help. It works!