erro using celldex, plzzzzzz help me

[tingchen0102-cell]

library(celldex)

get reference data -----------

ref <- celldex::HumanPrimaryCellAtlasData()
/Users/tinghuan/Library/Caches/org.R-project.R/R/ExperimentHub
does not exist, create directory? (yes/no):
/Users/tinghuan/Library/Caches/org.R-project.R/R/ExperimentHub
does not exist, create directory? (yes/no): yes
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) :
bfcadd() failed; see warnings()
In addition: Warning messages:
1: download failed
web resource path: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’
local file path: ‘/Users/tinghuan/Library/Caches/org.R-project.R/R/ExperimentHub/3751a571f30_experimenthub.sqlite3’
reason: length(keys) == length(values) is not TRUE
2: bfcadd() failed; resource removed
rid: BFC1
fpath: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’
reason: download failed

[lshep]

I'm not able to reproduce this locally.

> ref <- celldex::HumanPrimaryCellAtlasData()
> ref
class: SummarizedExperiment 
dim: 19363 713 
metadata(0):
assays(1): logcounts
rownames(19363): A1BG A1BG-AS1 ... ZZEF1 ZZZ3
rowData names(0):
colnames(713): GSM112490 GSM112491 ... GSM92233 GSM92234
colData names(3): label.main label.fine label.ont

Please include your sessionInfo:

library(celldex)
sessionInfo()

Are you at an institution that is behind a proxy or a firewall that could be prevent access?

[tingchen0102-cell]

hi here is it m thanks a lot!!!

library(celldex)
sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] SingleR_2.4.1 celldex_1.12.0 SummarizedExperiment_1.32.0
[4] Biobase_2.62.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.8
[7] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1
[10] MatrixGenerics_1.14.0 matrixStats_1.5.0

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_2.0.0
[4] magrittr_2.0.3 spatstat.utils_3.1-4 farver_2.1.2
[7] zlibbioc_1.48.2 vctrs_0.6.5 ROCR_1.0-11
[10] spatstat.explore_3.4-3 memoise_2.0.1 DelayedMatrixStats_1.24.0
[13] RCurl_1.98-1.17 htmltools_0.5.8.1 S4Arrays_1.2.1
[16] AnnotationHub_3.10.1 curl_6.4.0 SparseArray_1.2.4
[19] sctransform_0.4.2 parallelly_1.45.0 KernSmooth_2.23-26
[22] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9
[25] plotly_4.11.0 zoo_1.8-14 cachem_1.1.0
[28] igraph_2.1.4 mime_0.13 lifecycle_1.0.4
[31] pkgconfig_2.0.3 rsvd_1.0.5 Matrix_1.6-5
[34] R6_2.6.1 fastmap_1.2.0 GenomeInfoDbData_1.2.11
[37] fitdistrplus_1.2-4 future_1.40.0 shiny_1.11.1
[40] digest_0.6.37 patchwork_1.3.1 AnnotationDbi_1.64.1
[43] tensor_1.5.1 Seurat_5.2.1 RSpectra_0.16-2
[46] irlba_2.3.5.1 ExperimentHub_2.10.0 RSQLite_2.4.2
[49] beachmat_2.18.1 filelock_1.0.3 progressr_0.15.1
[52] spatstat.sparse_3.1-0 polyclip_1.10-7 httr_1.4.7
[55] abind_1.4-8 compiler_4.3.3 bit64_4.6.0-1
[58] withr_3.0.2 BiocParallel_1.36.0 DBI_1.2.3
[61] fastDummies_1.7.5 MASS_7.3-60.0.1 rappdirs_0.3.3
[64] DelayedArray_0.28.0 tools_4.3.3 lmtest_0.9-40
[67] interactiveDisplayBase_1.40.0 httpuv_1.6.16 future.apply_1.11.3
[70] goftest_1.2-3 glue_1.8.0 nlme_3.1-168
[73] promises_1.3.3 grid_4.3.3 Rtsne_0.17
[76] reshape2_1.4.4 cluster_2.1.8.1 generics_0.1.4
[79] spatstat.data_3.1-6 gtable_0.3.6 tidyr_1.3.1
[82] data.table_1.17.8 BiocSingular_1.18.0 ScaledMatrix_1.10.0
[85] sp_2.2-0 XVector_0.42.0 spatstat.geom_3.4-1
[88] RcppAnnoy_0.0.22 stringr_1.5.1 ggrepel_0.9.6
[91] RANN_2.6.2 BiocVersion_3.18.1 pillar_1.11.0
[94] spam_2.11-1 RcppHNSW_0.6.0 later_1.4.2
[97] splines_4.3.3 dplyr_1.1.4 BiocFileCache_2.10.2
[100] lattice_0.22-7 deldir_2.0-4 survival_3.8-3
[103] bit_4.6.0 tidyselect_1.2.1 Biostrings_2.70.3
[106] miniUI_0.1.2 pbapply_1.7-2 gridExtra_2.3
[109] scattermore_1.2 stringi_1.8.7 lazyeval_0.2.2
[112] yaml_2.3.10 codetools_0.2-20 tibble_3.3.0
[115] BiocManager_1.30.26 cli_3.6.5 uwot_0.2.3
[118] reticulate_1.42.0 xtable_1.8-4 Rcpp_1.1.0
[121] spatstat.random_3.4-1 globals_0.17.0 dbplyr_2.5.0
[124] png_0.1-8 spatstat.univar_3.1-3 parallel_4.3.3
[127] ggplot2_3.5.2 blob_1.2.4 dotCall64_1.2
[130] sparseMatrixStats_1.14.0 bitops_1.0-9 listenv_0.9.1
[133] viridisLite_0.4.2 scales_1.4.0 ggridges_0.5.6
[136] SeuratObject_5.1.0 purrr_1.0.4 crayon_1.5.3
[139] rlang_1.1.6 cowplot_1.2.0 KEGGREST_1.42.0

[tingchen0102-cell]

Are you at an institution that is behind a proxy or a firewall that could be prevent access?
Ans: in fact , yes i am at an institution, could it be? how can i fix it?

[lshep]

What version of Bioconductor are you using? 3.20?

[tingchen0102-cell]

3.18 i beliveve

[lshep]

Please confirm with

BiocManager::version()

Can you also try the following:

download.file("https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3", 
              destfile = tempfile(), 
              method = "libcurl")

[tingchen0102-cell]

BiocManager::version()
[1] ‘3.18’

[tingchen0102-cell]

> download.file("https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3", 
+               destfile = tempfile(), 
+               method = "libcurl")
trying URL 'https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3'
Content type 'application/octet-stream' length 9698304 bytes (9.2 MB)
==================================================
downloaded 9.2 MB

[tingchen0102-cell]

i tried

[tingchen0102-cell]

still giving me erro like this :

ref <- celldex::HumanPrimaryCellAtlasData()
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) :
bfcadd() failed; see warnings()
In addition: Warning messages:
1: download failed
web resource path: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’
local file path: ‘/Users/tinghuan/Library/Caches/org.R-project.R/R/ExperimentHub/3751eac35df_experimenthub.sqlite3’
reason: length(keys) == length(values) is not TRUE
2: bfcadd() failed; resource removed
rid: BFC2
fpath: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’
reason: download failed

[lshep]

can you try the following:

library(ExperimentHub)
eh = ExperimentHub()
# if it errors
traceback()

[tingchen0102-cell]

yes

library(ExperimentHub)
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: ‘AnnotationHub’

The following object is masked from ‘package:Biobase’:

cache

eh = ExperimentHub()
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) :
bfcadd() failed; see warnings()
In addition: Warning messages:
1: download failed
web resource path: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’
local file path: ‘/Users/tinghuan/Library/Caches/org.R-project.R/R/ExperimentHub/3756dc1aa0e_experimenthub.sqlite3’
reason: length(keys) == length(values) is not TRUE
2: bfcadd() failed; resource removed
rid: BFC3
fpath: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’
reason: download failed

if it errors

traceback()
8: stop(call, " failed; see warnings()")
7: .util_download(x, rid[i], proxy, config, "bfcadd()", ...)
6: bfcadd(bfc, rname = paste0(tolower(.class), ".sqlite3"), fpath = remote_db,
proxy = proxy)
5: bfcadd(bfc, rname = paste0(tolower(.class), ".sqlite3"), fpath = remote_db,
proxy = proxy)
4: .updateHubDB(hub_bfc, .class, url, proxy, localHub)
3: .create_cache(.class, url, cache, proxy, localHub, ask)
2: .Hub("ExperimentHub", hub, cache, proxy, localHub, ask, ...)
1: ExperimentHub()

if it errors

[lshep]

BiocManager::valid() 
# if there is updates need please do them you can also do 
BiocManager::install()

#  then lets remove and reinitialize the cache

unlink("/Users/tinghuan/Library/Caches/org.R-project.R/R/ExperimentHub", recursive=TRUE)
library(ExperimentHub)
eh <- ExperimentHub()

[tingchen0102-cell]

hi Ishep, I have gone that still doesn't work, very weird, hm

[lshep]

See if its the default cache location:

hub <- ExperimentHub(cache = tempdir())

If that still doesn't work the institution or proxy may be interfering.

https://bioconductor.org/packages/3.20/bioc/vignettes/AnnotationHub/inst/doc/TroubleshootingTheHubs.html#accessing-behind-a-proxy

Provides instructions for setting it but you may need to get information from IT