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chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census
https://chanzuckerberg.github.io/cellxgene-census/
MIT License
88 stars 22 forks source link

[R] cellxgene-census `PermanentRedirect` S3 error #1261

Open JHYSiu opened 3 months ago

JHYSiu commented 3 months ago

When trying to access cell-census, I can open_soma fine but then when I try to explore or pull data following the tutorial, I get this error: 

Error: S3: Error while listing with prefix 's3://cellxgene-census-public-us-west-2/cell-census/2024-07-01/soma/$
ensus_data/homo_sapiens/__schema/' and delimiter '/'[Error Type: 100] [HTTP Response Code: 301] [Exception: Per$
anentRedirect] [Remote IP: 52.217.13.168] [Request ID: SAXZR0MF9NWDNTTK] [Headers: 'content-type' = 'applicatio$
/xml' 'date' = 'Wed, 14 Aug 2024 12:27:00 GMT' 'server' = 'AmazonS3' 'transfer-encoding' = 'chunked' 'x-amz-buc$
et-region' = 'us-west-2' 'x-amz-id-2' = 'AV3lMM1aGM0Y3Q3Cf7oA4BMsUrObIGEZvvCdbftnUlrrzofgY+tcZHurJN/WnD06ickn4+$
yUvA=' 'x-amz-request-id' = 'SAXZR0MF9NWDNTTK'] : Unable to parse ExceptionName: PermanentRedirect Message: The 
bucket you are attempting to access must be addressed using the specified endpoint. Please send all future requ$
sts to this endpoint.

(It's similar to the issue described here I think: https://github.com/chanzuckerberg/cellxgene-census/issues/908)

sessionInfo() R version 4.2.1 (2022-06-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /gpfs3/apps/eb/2020b/skylake/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64/libflexiblas.so.3.2

locale: [1] C

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

other attached packages: [1] RcppSpdlog_0.0.17 qs_0.26.3
[3] cellxgene.census_1.15.0 SingleCellExperiment_1.20.1 [5] SummarizedExperiment_1.28.0 Biobase_2.58.0
[7] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[9] IRanges_2.32.0 S4Vectors_0.36.2
[11] BiocGenerics_0.44.0 MatrixGenerics_1.10.0
[13] matrixStats_1.3.0

loaded via a namespace (and not attached): [1] zoo_1.8-12 tidyselect_1.2.1 purrr_1.0.2
[4] lattice_0.20-45 vctrs_0.6.5 generics_0.1.3
[7] base64enc_0.1-3 utf8_1.2.4 rlang_1.1.4
[10] pillar_1.9.0 glue_1.7.0 aws.s3_0.3.21
[13] bit64_4.0.5 GenomeInfoDbData_1.2.9 lifecycle_1.0.4
[16] zlibbioc_1.44.0 stringfish_0.16.0 RApiSerialize_0.1.3
[19] arrow_16.1.0 tiledbsoma_1.13.0 nanoarrow_0.5.0.1
[22] curl_5.2.1 fansi_1.0.6 urltools_1.7.3
[25] triebeard_0.4.1 Rcpp_1.0.13 DelayedArray_0.24.0
[28] tiledb_0.29.0 RcppCCTZ_0.2.12 RcppParallel_5.1.8
[31] jsonlite_1.8.8 XVector_0.38.0 fs_1.6.4
[34] bit_4.0.5 digest_0.6.36 dplyr_1.1.4
[37] grid_4.2.1 cli_3.6.3 tools_4.2.1
[40] bitops_1.0-8 magrittr_2.0.3 RCurl_1.98-1.16
[43] tibble_3.2.1 spdl_0.0.5 aws.signature_0.6.0
[46] pkgconfig_2.0.3 Matrix_1.6-4 data.table_1.15.4
[49] xml2_1.3.6 nanotime_0.3.9 assertthat_0.2.1
[52] httr_1.4.7 R6_2.5.1 compiler_4.2.1

ebezzi commented 3 months ago

Hey @JHYSiu,

Thanks for reporting this. It would be useful if you could paste the exact code that causes this issue. In particular, are you overriding the default configuration when calling open_soma?

JHYSiu commented 3 months ago

Sorry, here it is. 

census <- open_soma(census_version = "2024-07-01")
cell_metadata <-  census$get("census_data")$get("homo_sapiens")$get("obs")
ebezzi commented 3 months ago

Thanks, I can reproduce the issue. I filed a ticket in the tiledbsoma repo: https://github.com/single-cell-data/TileDB-SOMA/issues/2899

Note that this issue seems to only appear if you try to inspect the SOMACollection object, but you should still be able to query it and convert it to (e.g.) an R dataframe without encountering this issue, as shown in the tutorial.

johnkerl commented 3 months ago

As a workaround -- maybe not acceptable, but as an option -- you can set environment variables.

export AWS_ACCESS_KEY_ID="whatever"
export AWS_SECRET_ACCESS_KEY="whatever"
export AWS_DEFAULT_REGION="us-west-2"
ivirshup commented 3 months ago

@johnkerl @ebezzi do you know if these are related to the current CI failures for R? It looks like the same error, but I'm not sure it it being the same cause makes sense.

https://github.com/chanzuckerberg/cellxgene-census/actions/runs/10409767192/job/28830126754

johnkerl commented 3 months ago

@ivirshup looks the same to me ... will it be possible t use the workaround of setting the environment variable

export AWS_DEFAULT_REGION="us-west-2"

?

ryan-williams commented 2 months ago

Here are two R notebooks:

The first shows the error, the second shows that it can be worked around with:

Sys.setenv(AWS_DEFAULT_REGION = "us-west-2")

export AWS_DEFAULT_REGION=us-west-2 outside the notebook also works, and is likely what most users will want to do.

census-region-failure.ipynb also shows two us-west-2 configs that are apparently not propagating correctly:

  1. vfs.s3.region = "us-west-2" in new_SOMATileDBContext_for_census
  2. region = "us-west-2" in ~/.aws/config default profile
    • Verifying: aws configure get region returns us-west-2

Seems likely there are bugs somewhere in the stack, causing these to not work (and explicit $AWS_DEFAULT_REGION to be required).

ivirshup commented 2 months ago

@ryan-williams I still see this error after setting the environment variable and running:

library(cellxgene.census)
library(SingleCellExperiment)

census = open_soma()

sce_obj = get_single_cell_experiment(
  census, "Homo sapiens",
  obs_column_names = c("cell_type", "tissue_general", "disease", "sex"),
  var_value_filter = "feature_id %in% c('ENSG00000161798', 'ENSG00000188229')",
  obs_value_filter = "cell_type == 'B cell' & tissue_general == 'lung' & disease == 'COVID-19'"
)

Here is a CI run that fails: https://github.com/chanzuckerberg/cellxgene-census/actions/runs/10728627156/job/29753546340?pr=1273

ryan-williams commented 2 months ago

@ivirshup in your log I see:

[HTTP Response Code: 403] [Exception: InvalidAccessKeyId]

Seems like a different issue than OP and I were seeing:

[HTTP Response Code: 301] [Exception: PermanentRedirect]

Can you verify that the credentials being used there can run e.g.:

aws s3 ls s3://cellxgene-census-public-us-west-2/cell-census/2024-09-02/soma/census_info/datasets/

Maybe try putting that earlier in the GHA (ideally before the 41min step…), and re-running?

hlmtran commented 1 month ago

Has there been any update on this issue? I am suffering from a similar issue but immediately from using open_soma(). Setting the environment variable does not help.

Sys.setenv(AWS_DEFAULT_REGION =  #"us-west-2")
census <- open_soma(census_version = "2023-12-15")

Error: [TileDB::Task] Error: Caught std::exception: S3: Error while listing with prefix 's3://cellxgene-census-public-us-west-2/cell-census/2024-09-02/soma/census_info/datasets/' and delimiter '/'[Error Type: 100] [HTTP Response Code: 301] [Exception: PermanentRedirect] [Remote IP: 52.216.215.66] [Request ID: VY0G087PD45KK1G7] [Headers: 'content-type' = 'application/xml' 'date' = 'Wed, 09 Oct 2024 21:04:29 GMT' 'server' = 'AmazonS3' 'transfer-encoding' = 'chunked' 'x-amz-bucket-region' = 'us-west-2' 'x-amz-id-2' = 'S29CB1wdkNKHzmbYNd44B9+jVJQnIFc4biQIy4Y/baXaqqZ/4gIyJwX0YE1w+MX0l8aR5lnxmqU=' 'x-amz-request-id' = 'VY0G087PD45KK1G7'] : Unable to parse ExceptionName: PermanentRedirect Message: The bucket you are attempting to access must be addressed using the specified endpoint. Please send all future requests to this endpoint. 

R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: AlmaLinux 9.4 (Seafoam Ocelot)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.21.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=C.utf8       LC_NUMERIC=C          LC_TIME=C.utf8        LC_COLLATE=C.utf8     LC_MONETARY=C.utf8    LC_MESSAGES=C.utf8   
 [7] LC_PAPER=C.utf8       LC_NAME=C             LC_ADDRESS=C          LC_TELEPHONE=C        LC_MEASUREMENT=C.utf8 LC_IDENTIFICATION=C  

time zone: UTC
tzcode source: internal

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

other attached packages:
[1] RcppSpdlog_0.0.18       cellxgene.census_1.16.1

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.4.0               later_1.3.2                 aws.s3_0.3.21               urltools_1.7.3             
  [6] tibble_3.2.1                triebeard_0.4.1             polyclip_1.10-7             fastDummies_1.7.4           lifecycle_1.0.4            
 [11] globals_0.16.3              lattice_0.22-6              MASS_7.3-61                 magrittr_2.0.3              limma_3.60.6               
 [16] plotly_4.10.4               rmarkdown_2.28              yaml_2.3.10                 httpuv_1.6.15               Seurat_5.1.0               
 [21] tiledbsoma_1.14.3           sctransform_0.4.1           spam_2.11-0                 sp_2.1-4                    spatstat.sparse_3.1-0      
 [26] reticulate_1.39.0           cowplot_1.1.3               pbapply_1.7-2               DBI_1.2.3                   RColorBrewer_1.1-3         
 [31] abind_1.4-8                 zlibbioc_1.50.0             Rtsne_0.17                  GenomicRanges_1.56.1        purrr_1.0.2                
 [36] BiocGenerics_0.50.0         msigdbr_7.5.1               GenomeInfoDbData_1.2.12     IRanges_2.38.1              S4Vectors_0.42.1           
 [41] ggrepel_0.9.6               irlba_2.3.5.1               listenv_0.9.1               spatstat.utils_3.1-0        goftest_1.2-3              
 [46] RSpectra_0.16-2             spatstat.random_3.3-2       fitdistrplus_1.2-1          parallelly_1.38.0           leiden_0.4.3.1             
 [51] codetools_0.2-20            DelayedArray_0.30.1         xml2_1.3.6                  tidyselect_1.2.1            UCSC.utils_1.0.0           
 [56] farver_2.1.2                matrixStats_1.4.1           stats4_4.4.0                base64enc_0.1-3             spatstat.explore_3.3-2     
 [61] jsonlite_1.8.9              progressr_0.14.0            ggridges_0.5.6              survival_3.7-0              tools_4.4.0                
 [66] tiledb_0.30.2               ica_1.0-3                   Rcpp_1.0.13                 glue_1.8.0                  spdl_0.0.5                 
 [71] gridExtra_2.3               SparseArray_1.4.8           xfun_0.48                   MatrixGenerics_1.16.0       GenomeInfoDb_1.40.1        
 [76] dplyr_1.1.4                 BiocManager_1.30.25         fastmap_1.2.0               fansi_1.0.6                 RcppML_0.5.6               
 [81] digest_0.6.37               R6_2.5.1                    mime_0.12                   colorspace_2.1-1            scattermore_1.2            
 [86] tensor_1.5                  RcppCCTZ_0.2.12             spatstat.data_3.1-2         RSQLite_2.3.7               utf8_1.2.4                 
 [91] tidyr_1.3.1                 generics_0.1.3              data.table_1.16.0           httr_1.4.7                  htmlwidgets_1.6.4          
 [96] S4Arrays_1.4.1              uwot_0.2.2                  pkgconfig_2.0.3             gtable_0.3.5                blob_1.2.4                 
[101] lmtest_0.9-40               SingleCellExperiment_1.26.0 XVector_0.44.0              htmltools_0.5.8.1           dotCall64_1.2              
[106] fgsea_1.31.3                SeuratObject_5.0.2          scales_1.3.0                Biobase_2.64.0              png_0.1-8                  
[111] spatstat.univar_3.0-1       knitr_1.48                  rstudioapi_0.16.0           reshape2_1.4.4              nlme_3.1-166               
[116] curl_5.2.3                  cachem_1.1.0                zoo_1.8-12                  stringr_1.5.1               KernSmooth_2.23-24         
[121] parallel_4.4.0              miniUI_0.1.1.1              arrow_17.0.0.1              AnnotationDbi_1.66.0        nanotime_0.3.10            
[126] pillar_1.9.0                grid_4.4.0                  vctrs_0.6.5                 nanoarrow_0.5.0.1           RANN_2.6.2                 
[131] promises_1.3.0              xtable_1.8-4                cluster_2.1.6               evaluate_1.0.0              cli_3.6.3                  
[136] singlet_0.99.6              compiler_4.4.0              rlang_1.1.4                 crayon_1.5.3                future.apply_1.11.2        
[141] aws.signature_0.6.0         fs_1.6.4                    plyr_1.8.9                  stringi_1.8.4               viridisLite_0.4.2          
[146] deldir_2.0-4                BiocParallel_1.38.0         assertthat_0.2.1            babelgene_22.9              munsell_0.5.1              
[151] Biostrings_2.72.1           lazyeval_0.2.2              spatstat.geom_3.3-3         Matrix_1.7-0                RcppHNSW_0.6.0             
[156] patchwork_1.3.0             bit64_4.5.2                 future_1.34.0               ggplot2_3.5.1               KEGGREST_1.44.1            
[161] statmod_1.5.0               shiny_1.9.1                 SummarizedExperiment_1.34.0 ROCR_1.0-11                 igraph_2.0.3               
[166] memoise_2.0.1               fastmatch_1.1-4             bit_4.5.0
hlmtran commented 1 month ago

Has there been any update on this issue? I am suffering from a similar issue but immediately from using open_soma(). Setting the environment variable does not help.

Sys.setenv(AWS_DEFAULT_REGION =  #"us-west-2")
census <- open_soma(census_version = "2023-12-15")

Error: [TileDB::Task] Error: Caught std::exception: S3: Error while listing with prefix 's3://cellxgene-census-public-us-west-2/cell-census/2024-09-02/soma/census_info/datasets/' and delimiter '/'[Error Type: 100] [HTTP Response Code: 301] [Exception: PermanentRedirect] [Remote IP: 52.216.215.66] [Request ID: VY0G087PD45KK1G7] [Headers: 'content-type' = 'application/xml' 'date' = 'Wed, 09 Oct 2024 21:04:29 GMT' 'server' = 'AmazonS3' 'transfer-encoding' = 'chunked' 'x-amz-bucket-region' = 'us-west-2' 'x-amz-id-2' = 'S29CB1wdkNKHzmbYNd44B9+jVJQnIFc4biQIy4Y/baXaqqZ/4gIyJwX0YE1w+MX0l8aR5lnxmqU=' 'x-amz-request-id' = 'VY0G087PD45KK1G7'] : Unable to parse ExceptionName: PermanentRedirect Message: The bucket you are attempting to access must be addressed using the specified endpoint. Please send all future requests to this endpoint.

R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: AlmaLinux 9.4 (Seafoam Ocelot)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.21.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=C.utf8       LC_NUMERIC=C          LC_TIME=C.utf8        LC_COLLATE=C.utf8     LC_MONETARY=C.utf8    LC_MESSAGES=C.utf8   
 [7] LC_PAPER=C.utf8       LC_NAME=C             LC_ADDRESS=C          LC_TELEPHONE=C        LC_MEASUREMENT=C.utf8 LC_IDENTIFICATION=C  

time zone: UTC
tzcode source: internal

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

other attached packages:
[1] RcppSpdlog_0.0.18       cellxgene.census_1.16.1

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.4.0               later_1.3.2                 aws.s3_0.3.21               urltools_1.7.3             
  [6] tibble_3.2.1                triebeard_0.4.1             polyclip_1.10-7             fastDummies_1.7.4           lifecycle_1.0.4            
 [11] globals_0.16.3              lattice_0.22-6              MASS_7.3-61                 magrittr_2.0.3              limma_3.60.6               
 [16] plotly_4.10.4               rmarkdown_2.28              yaml_2.3.10                 httpuv_1.6.15               Seurat_5.1.0               
 [21] tiledbsoma_1.14.3           sctransform_0.4.1           spam_2.11-0                 sp_2.1-4                    spatstat.sparse_3.1-0      
 [26] reticulate_1.39.0           cowplot_1.1.3               pbapply_1.7-2               DBI_1.2.3                   RColorBrewer_1.1-3         
 [31] abind_1.4-8                 zlibbioc_1.50.0             Rtsne_0.17                  GenomicRanges_1.56.1        purrr_1.0.2                
 [36] BiocGenerics_0.50.0         msigdbr_7.5.1               GenomeInfoDbData_1.2.12     IRanges_2.38.1              S4Vectors_0.42.1           
 [41] ggrepel_0.9.6               irlba_2.3.5.1               listenv_0.9.1               spatstat.utils_3.1-0        goftest_1.2-3              
 [46] RSpectra_0.16-2             spatstat.random_3.3-2       fitdistrplus_1.2-1          parallelly_1.38.0           leiden_0.4.3.1             
 [51] codetools_0.2-20            DelayedArray_0.30.1         xml2_1.3.6                  tidyselect_1.2.1            UCSC.utils_1.0.0           
 [56] farver_2.1.2                matrixStats_1.4.1           stats4_4.4.0                base64enc_0.1-3             spatstat.explore_3.3-2     
 [61] jsonlite_1.8.9              progressr_0.14.0            ggridges_0.5.6              survival_3.7-0              tools_4.4.0                
 [66] tiledb_0.30.2               ica_1.0-3                   Rcpp_1.0.13                 glue_1.8.0                  spdl_0.0.5                 
 [71] gridExtra_2.3               SparseArray_1.4.8           xfun_0.48                   MatrixGenerics_1.16.0       GenomeInfoDb_1.40.1        
 [76] dplyr_1.1.4                 BiocManager_1.30.25         fastmap_1.2.0               fansi_1.0.6                 RcppML_0.5.6               
 [81] digest_0.6.37               R6_2.5.1                    mime_0.12                   colorspace_2.1-1            scattermore_1.2            
 [86] tensor_1.5                  RcppCCTZ_0.2.12             spatstat.data_3.1-2         RSQLite_2.3.7               utf8_1.2.4                 
 [91] tidyr_1.3.1                 generics_0.1.3              data.table_1.16.0           httr_1.4.7                  htmlwidgets_1.6.4          
 [96] S4Arrays_1.4.1              uwot_0.2.2                  pkgconfig_2.0.3             gtable_0.3.5                blob_1.2.4                 
[101] lmtest_0.9-40               SingleCellExperiment_1.26.0 XVector_0.44.0              htmltools_0.5.8.1           dotCall64_1.2              
[106] fgsea_1.31.3                SeuratObject_5.0.2          scales_1.3.0                Biobase_2.64.0              png_0.1-8                  
[111] spatstat.univar_3.0-1       knitr_1.48                  rstudioapi_0.16.0           reshape2_1.4.4              nlme_3.1-166               
[116] curl_5.2.3                  cachem_1.1.0                zoo_1.8-12                  stringr_1.5.1               KernSmooth_2.23-24         
[121] parallel_4.4.0              miniUI_0.1.1.1              arrow_17.0.0.1              AnnotationDbi_1.66.0        nanotime_0.3.10            
[126] pillar_1.9.0                grid_4.4.0                  vctrs_0.6.5                 nanoarrow_0.5.0.1           RANN_2.6.2                 
[131] promises_1.3.0              xtable_1.8-4                cluster_2.1.6               evaluate_1.0.0              cli_3.6.3                  
[136] singlet_0.99.6              compiler_4.4.0              rlang_1.1.4                 crayon_1.5.3                future.apply_1.11.2        
[141] aws.signature_0.6.0         fs_1.6.4                    plyr_1.8.9                  stringi_1.8.4               viridisLite_0.4.2          
[146] deldir_2.0-4                BiocParallel_1.38.0         assertthat_0.2.1            babelgene_22.9              munsell_0.5.1              
[151] Biostrings_2.72.1           lazyeval_0.2.2              spatstat.geom_3.3-3         Matrix_1.7-0                RcppHNSW_0.6.0             
[156] patchwork_1.3.0             bit64_4.5.2                 future_1.34.0               ggplot2_3.5.1               KEGGREST_1.44.1            
[161] statmod_1.5.0               shiny_1.9.1                 SummarizedExperiment_1.34.0 ROCR_1.0-11                 igraph_2.0.3               
[166] memoise_2.0.1               fastmatch_1.1-4             bit_4.5.0

I think this post was scary enough that everything started working properly now.

dtatarak commented 1 month ago 
census <- open_soma(census_version = "2023-12-15")

I have this exact issue and none of the solutions here have worked. Has anyone figured out how to fix this?

johnkerl commented 1 month ago

@dtatarak thank you and our apologies.

The underlying is being actively worked. It turns out to have been more subtle than I had anticipated.

The workaround I've used successfully in the interim is:

Sys.setenv(TILEDB_VFS_S3_REGION = "us-west-2")
Sys.setenv(TILEDB_VFS_S3_NO_SIGN_REQUEST = "true")
dtatarak commented 1 month ago

@dtatarak thank you and our apologies.

The underlying is being actively worked. It turns out to have been more subtle than I had anticipated.

The workaround I've used successfully in the interim is:

Sys.setenv(TILEDB_VFS_S3_REGION = "us-west-2")
Sys.setenv(TILEDB_VFS_S3_NO_SIGN_REQUEST = "true")

@johnkerl

Thanks for the quick reply. Sadly that workaround does not fix the problem on my end.

Sys.setenv(TILEDB_VFS_S3_REGION = "us-west-2")
Sys.setenv(TILEDB_VFS_S3_NO_SIGN_REQUEST = "true")
census <- open_soma(census_version = "2023-12-15")

Still get this error:

Error: [TileDB::Task] Error: Caught std::exception: S3: Error while listing with prefix 's3://cellxgene-census-public-us-west-2/cell-census/2023-12-15/soma/' and delimiter '/'[Error Type: 100] [HTTP Response Code: 301] [Exception: PermanentRedirect] [Remote IP: 52.216.186.62] [Request ID: E5Q954P5JJWD68ZM] [Headers: 'content-type' = 'application/xml' 'date' = 'Wed, 23 Oct 2024 15:04:22 GMT' 'server' = 'AmazonS3' 'transfer-encoding' = 'chunked' 'x-amz-bucket-region' = 'us-west-2' 'x-amz-id-2' = 'qFZu73Vv/Nd/P1Kswi9n4N+0O1//6W1W9D08PtHi3dOiO/HpxiB22o28i1K1YPeM/QfT+nbEC5c=' 'x-amz-request-id' = 'E5Q954P5JJWD68ZM'] : Unable to parse ExceptionName: PermanentRedirect Message: The bucket you are attempting to access must be addressed using the specified endpoint. Please send all future requests to this endpoint.

johnkerl commented 1 month ago

Thanks for your patience @dtatarak . It's puzzling me that this workaround suffices for me but not you. :|

Can I trouble you to try one more thing?

Sys.setenv(TILEDB_VFS_S3_REGION = "us-west-2")
Sys.setenv(AWS_DEFAULT_REGION = "us-west-2")
Sys.setenv(TILEDB_VFS_S3_NO_SIGN_REQUEST = "true")

Also: can you try this after quitting and restarting R, and before doing library(tiledbsoma) and/or library(cellxgene.census)?

dtatarak commented 1 month ago

@johnkerl

Ah! Success! I had tried both of those workarounds separately but never together. Thank you very much!

johnkerl commented 1 month ago

Fantastic, thank you @dtatarak ! We are working on the real fix as a priority but I'm happy to hear you have a workaround in the interim.