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rnabioco / raer

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments
https://rnabioco.github.io/raer/
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Cannot connect to ExperimentHub server #120

Closed shmmuzhangh closed 3 months ago

shmmuzhangh commented 3 months ago

pbmc <- pbmc_10x() Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use error in .updateHubDB(hub_bfc, .class, url, proxy, localHub): Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE'

shmmuzhangh commented 3 months ago

pbmc <- pbmc_10x() Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use error in .updateHubDB(hub_bfc, .class, url, proxy, localHub): Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE'

When I tried this command, readLines("https://experimenthub.bioconductor.org/"), An error was shown. Error in file(con, "r"): cannot open the connection to 'https://experimenthub.bioconductor.org' In file(con, "r") : URL 'https://experimenthub.bioconductor.org/': status was 'SSL connect error' But I can access https://experimenthub.bioconductor.org/ in the browser of Chrome.

The issue happens when I use the latest R 4.4.1 software with the latest ExperimentHub. No proxy used.

jayhesselberth commented 3 months ago

This worked fine for me, might be a local internet issue.

> library(raerdata)
> raerdata::pbmc_10x()
  |===================================================| 100%

snapshotDate(): 2024-04-29
see ?raerdata and browseVignettes('raerdata') for documentation
downloading 1 resources
retrieving 1 resource
  |===================================================| 100%

loading from cache
see ?raerdata and browseVignettes('raerdata') for documentation
downloading 1 resources
retrieving 1 resource
  |===================================================| 100%

loading from cache
see ?raerdata and browseVignettes('raerdata') for documentation
downloading 1 resources
retrieving 1 resource
  |===================================================| 100%

loading from cache
require(“GenomicRanges”)
see ?raerdata and browseVignettes('raerdata') for documentation
downloading 1 resources
retrieving 1 resource
  |===================================================| 100%

loading from cache
require(“SingleCellExperiment”)
$bam
class: BamFile 
path: /Users/jayhesselberth/Library/Cach.../524e41751cb2_8311
index: /Users/jayhesselberth/Library/Cac.../524e6faf0bb0_8312
isOpen: FALSE 
yieldSize: NA 
obeyQname: FALSE 
asMates: FALSE 
qnamePrefixEnd: NA 
qnameSuffixStart: NA 

$sites
GRanges object with 15638648 ranges and 0 metadata columns:
             seqnames    ranges strand
                <Rle> <IRanges>  <Rle>
         [1]     chr1     87158      -
         [2]     chr1     87168      -
         [3]     chr1     87171      -
         [4]     chr1     87189      -
         [5]     chr1     87218      -
         ...      ...       ...    ...
  [15638644]     chrY  56885715      +
  [15638645]     chrY  56885716      +
  [15638646]     chrY  56885728      +
  [15638647]     chrY  56885841      +
  [15638648]     chrY  56885850      +
  -------
  seqinfo: 44 sequences from hg38 genome; no seqlengths

$sce
class: SingleCellExperiment 
dim: 36601 500 
metadata(2): Samples mkrs
assays(2): counts logcounts
rownames(36601): MIR1302-2HG FAM138A ... AC007325.4
  AC007325.2
rowData names(3): ID Symbol Type
colnames(500): TGTTTGTCAGTTAGGG-1 ATCTCTACAAGCTACT-1
  ... GGGCGTTTCAGGACGA-1 CTATAGGAGATTGTGA-1
colData names(8): Sample Barcode ... r celltype
reducedDimNames(2): PCA UMAP
mainExpName: NULL
altExpNames(0):

> sessioninfo::session_info()
─ Session info ────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       macOS Sonoma 14.6
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Denver
 date     2024-07-09
 rstudio  2024.04.2+764 Chocolate Cosmos (desktop)
 pandoc   NA

─ Packages ────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-5     2016-07-21 [1] CRAN (R 4.4.0)
 AnnotationDbi          1.66.0    2024-06-16 [1] Bioconduc~
 AnnotationHub          3.12.0    2024-04-30 [1] Bioconduc~
 Biobase              * 2.64.0    2024-04-30 [1] Bioconduc~
 BiocFileCache          2.12.0    2024-04-30 [1] Bioconduc~
 BiocGenerics         * 0.50.0    2024-04-30 [1] Bioconduc~
 BiocIO                 1.14.0    2024-04-30 [1] Bioconduc~
 BiocManager            1.30.23   2024-05-04 [1] CRAN (R 4.4.0)
 BiocParallel           1.38.0    2024-04-30 [1] Bioconduc~
 BiocVersion            3.19.1    2024-04-22 [1] Bioconductor 3.19 (R 4.4.0)
 Biostrings             2.72.1    2024-06-02 [1] Bioconduc~
 bit                    4.0.5     2022-11-15 [1] CRAN (R 4.4.0)
 bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.4.0)
 bitops                 1.0-7     2021-04-24 [1] CRAN (R 4.4.0)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.4.0)
 BSgenome               1.72.0    2024-04-30 [1] Bioconduc~
 cachem                 1.1.0     2024-05-16 [1] CRAN (R 4.4.0)
 callr                  3.7.6     2024-03-25 [1] CRAN (R 4.4.0)
 cli                    3.6.3     2024-06-21 [1] CRAN (R 4.4.0)
 codetools              0.2-20    2024-03-31 [1] CRAN (R 4.4.1)
 crayon                 1.5.3     2024-06-20 [1] CRAN (R 4.4.0)
 curl                   5.2.1     2024-03-01 [1] CRAN (R 4.4.0)
 DBI                    1.2.3     2024-06-02 [1] CRAN (R 4.4.0)
 dbplyr                 2.5.0     2024-03-19 [1] CRAN (R 4.4.0)
 DelayedArray           0.30.1    2024-05-30 [1] Bioconduc~
 dplyr                  1.1.4     2023-11-17 [1] CRAN (R 4.4.0)
 ExperimentHub          2.12.0    2024-04-30 [1] Bioconduc~
 fansi                  1.0.6     2023-12-08 [1] CRAN (R 4.4.0)
 fastmap                1.2.0     2024-05-15 [1] CRAN (R 4.4.0)
 filelock               1.0.3     2023-12-11 [1] CRAN (R 4.4.0)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.4.0)
 GenomeInfoDb         * 1.40.1    2024-06-16 [1] Bioconduc~
 GenomeInfoDbData       1.2.12    2024-04-24 [1] Bioconductor
 GenomicAlignments      1.40.0    2024-04-30 [1] Bioconduc~
 GenomicFeatures        1.56.0    2024-04-30 [1] Bioconduc~
 GenomicRanges        * 1.56.1    2024-06-16 [1] Bioconduc~
 glue                   1.7.0     2024-01-09 [1] CRAN (R 4.4.0)
 httr                   1.4.7     2023-08-15 [1] CRAN (R 4.4.0)
 IRanges              * 2.38.0    2024-04-30 [1] Bioconduc~
 jsonlite               1.8.8     2023-12-04 [1] CRAN (R 4.4.0)
 KEGGREST               1.44.1    2024-06-19 [1] Bioconduc~
 lattice                0.22-6    2024-03-20 [1] CRAN (R 4.4.1)
 lifecycle              1.0.4     2023-11-07 [1] CRAN (R 4.4.0)
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.4.0)
 Matrix                 1.7-0     2024-04-26 [1] CRAN (R 4.4.1)
 MatrixGenerics       * 1.16.0    2024-04-30 [1] Bioconduc~
 matrixStats          * 1.3.0     2024-04-11 [1] CRAN (R 4.4.0)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.4.0)
 mime                   0.12      2021-09-28 [1] CRAN (R 4.4.0)
 pak                    0.7.2     2024-03-17 [1] CRAN (R 4.4.0)
 pillar                 1.9.0     2023-03-22 [1] CRAN (R 4.4.0)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.4.0)
 png                    0.1-8     2022-11-29 [1] CRAN (R 4.4.0)
 processx               3.8.4     2024-03-16 [1] CRAN (R 4.4.0)
 ps                     1.7.7     2024-07-02 [1] CRAN (R 4.4.0)
 purrr                  1.0.2     2023-08-10 [1] CRAN (R 4.4.0)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.4.0)
 raer                 * 1.3.0     2024-07-09 [1] Bioconductor
 raerdata             * 0.99.3    2024-07-09 [1] Github (rnabioco/raerdata@8fab809)
 rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.4.0)
 RCurl                  1.98-1.14 2024-01-09 [1] CRAN (R 4.4.0)
 restfulr               0.0.15    2022-06-16 [1] CRAN (R 4.4.0)
 rjson                  0.2.21    2022-01-09 [1] CRAN (R 4.4.0)
 rlang                  1.1.4     2024-06-04 [1] CRAN (R 4.4.0)
 Rsamtools              2.20.0    2024-04-30 [1] Bioconduc~
 RSQLite                2.3.7     2024-05-27 [1] CRAN (R 4.4.0)
 rstudioapi             0.16.0    2024-03-24 [1] CRAN (R 4.4.0)
 rtracklayer            1.64.0    2024-05-06 [1] Bioconduc~
 S4Arrays               1.4.1     2024-05-30 [1] Bioconduc~
 S4Vectors            * 0.42.0    2024-04-30 [1] Bioconduc~
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.4.0)
 SingleCellExperiment * 1.26.0    2024-04-30 [1] Bioconduc~
 SparseArray            1.4.8     2024-05-30 [1] Bioconduc~
 SummarizedExperiment * 1.34.0    2024-04-30 [1] Bioconduc~
 tibble                 3.2.1     2023-03-20 [1] CRAN (R 4.4.0)
 tidyselect             1.2.1     2024-03-11 [1] CRAN (R 4.4.0)
 UCSC.utils             1.0.0     2024-05-06 [1] Bioconduc~
 utf8                   1.2.4     2023-10-22 [1] CRAN (R 4.4.0)
 vctrs                  0.6.5     2023-12-01 [1] CRAN (R 4.4.0)
 withr                  3.0.0     2024-01-16 [1] CRAN (R 4.4.0)
 XML                    3.99-0.17 2024-06-25 [1] CRAN (R 4.4.0)
 XVector                0.44.0    2024-04-30 [1] Bioconduc~
 yaml                   2.3.8     2023-12-11 [1] CRAN (R 4.4.0)
 zlibbioc               1.50.0    2024-04-30 [1] Bioconduc~

 [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library

───────────────────────────────────────────────────────────
kriemo commented 3 months ago

I suspect this may be an issue with connecting to the ExperimentHub rather than an issue with the pbmc_10x() function from the raerdata data package. Do you get an error when you run ExperimentHub::ExperimentHub()?

shmmuzhangh commented 3 months ago

I suspect this may be an issue with connecting to the ExperimentHub rather than an issue with the pbmc_10x() function from the raerdata data package. Do you get an error when you run ExperimentHub::ExperimentHub()?

Many thanks. I have tried ExperimentHub::ExperimentHub() with the same reply of “cannot connect to ExperimentHub server”。 Is there a way to run it using local resources?

kriemo commented 3 months ago

There is an option to use resources offline (localHub=TRUE), however the resources need to have been already retrieved and in your local experiment hub cache.

If you can't access ExperimentHub while online, then I suggest making a post at https://support.bioconductor.org/ to get assistance with ExperimentHub access as that is the root issue here.

Feel free to reopen if you run into further issues after resolving Experimenthub access.