curl error with bfcrpath: HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)

[lcolladotor]

Hi BiocFileCache team,

Last week at BioC2023 I ran into some issues with spatialLIBD::fetch_data("spatialDLPFC_Visium_modeling_results") and related functions after I wiped out clean my BiocFileCache on my laptop and forced it to re-download data. I made a reprex below abstracting away the spatialLIBD layer.

library("BiocFileCache")
#> Loading required package: dbplyr
bfc <- BiocFileCache::BiocFileCache()
BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
#> adding rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1'
#> Warning in value[[3L]](cond): 
#> trying to add rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1' produced error:
#>   HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
#> Error in BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1"): not all 'rnames' found or unique.
traceback()
#> No traceback available
options(width = 120)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.1 (2023-06-16)
#>  os       macOS Ventura 13.4
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2023-08-11
#>  pandoc   3.1.5 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package       * version date (UTC) lib source
#>  BiocFileCache * 2.8.0   2023-04-25 [1] Bioconductor
#>  bit             4.0.5   2022-11-15 [1] CRAN (R 4.3.0)
#>  bit64           4.0.5   2020-08-30 [1] CRAN (R 4.3.0)
#>  blob            1.2.4   2023-03-17 [1] CRAN (R 4.3.0)
#>  cachem          1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
#>  cli             3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
#>  curl            5.0.1   2023-06-07 [1] CRAN (R 4.3.0)
#>  DBI             1.1.3   2022-06-18 [1] CRAN (R 4.3.0)
#>  dbplyr        * 2.3.3   2023-07-07 [1] CRAN (R 4.3.0)
#>  digest          0.6.33  2023-07-07 [1] CRAN (R 4.3.0)
#>  dplyr           1.1.2   2023-04-20 [1] CRAN (R 4.3.0)
#>  evaluate        0.21    2023-05-05 [1] CRAN (R 4.3.0)
#>  fansi           1.0.4   2023-01-22 [1] CRAN (R 4.3.0)
#>  fastmap         1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
#>  filelock        1.0.2   2018-10-05 [1] CRAN (R 4.3.0)
#>  fs              1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
#>  generics        0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
#>  glue            1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
#>  htmltools       0.5.5   2023-03-23 [1] CRAN (R 4.3.0)
#>  httr            1.4.6   2023-05-08 [1] CRAN (R 4.3.0)
#>  knitr           1.43    2023-05-25 [1] CRAN (R 4.3.0)
#>  lifecycle       1.0.3   2022-10-07 [1] CRAN (R 4.3.0)
#>  magrittr        2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>  memoise         2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
#>  pillar          1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>  pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  purrr           1.0.1   2023-01-10 [1] CRAN (R 4.3.0)
#>  R.cache         0.16.0  2022-07-21 [1] CRAN (R 4.3.0)
#>  R.methodsS3     1.8.2   2022-06-13 [1] CRAN (R 4.3.0)
#>  R.oo            1.25.0  2022-06-12 [1] CRAN (R 4.3.0)
#>  R.utils         2.12.2  2022-11-11 [1] CRAN (R 4.3.0)
#>  R6              2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  reprex          2.0.2   2022-08-17 [1] CRAN (R 4.3.0)
#>  rlang           1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
#>  rmarkdown       2.23    2023-07-01 [1] CRAN (R 4.3.0)
#>  RSQLite         2.3.1   2023-04-03 [1] CRAN (R 4.3.0)
#>  rstudioapi      0.15.0  2023-07-07 [1] CRAN (R 4.3.0)
#>  sessioninfo     1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>  styler          1.10.1  2023-06-05 [1] CRAN (R 4.3.0)
#>  tibble          3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tidyselect      1.2.0   2022-10-10 [1] CRAN (R 4.3.0)
#>  utf8            1.2.3   2023-01-31 [1] CRAN (R 4.3.0)
#>  vctrs           0.6.3   2023-06-14 [1] CRAN (R 4.3.0)
#>  withr           2.5.0   2022-03-03 [1] CRAN (R 4.3.0)
#>  xfun            0.39    2023-04-20 [1] CRAN (R 4.3.0)
#>  yaml            2.3.7   2023-01-23 [1] CRAN (R 4.3.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

^{Created on 2023-08-11 with reprex v2.0.2}

I was surprised by this as everything is working ok at GitHub actions using the biocthis workflow as well as in the Bioconductor BBS system.

In the 30 min prior to our spatialLIBD BioC2023 demo with @lahuuki, I tried resolving this. By googling the error message, I realized that curl (and httr), BiocFileCache dependencies, now use http version 2 instead of 1.1. See jeroen/curl#232 for a related issue. There they link to https://cran.r-project.org/web/packages/curl/vignettes/intro.html#Disabling_HTTP2 for disabling HTTP2, but I'm not sure if I can do that as a BiocFileCache user. Maybe through the config argument https://github.com/search?q=repo%3ABioconductor%2FBiocFileCache%20config&type=code. But that doesn't seem to be the case (maybe I'm not specifying config where I should):

> BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1", config = list(http_version = 2))
adding rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1'
  |==================================================================================| 100%

Error in BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1",  : 
  not all 'rnames' found or unique.
In addition: Warning message:
In value[[3L]](cond) : 
trying to add rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1' produced error:
  HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)

What I find weird is that the download does actually happen, but at the very end it errors out. So I'm not 100% sure that the error is related to the http version 1.1 vs 2 change.

Hm... maybe something else changed in BiocFileCache::bfcrpath() that I'm not aware of, but well, in that case, I would expect things to break on GitHub Actions and BBS as well.

1 to 3 students at https://github.com/lcolladotor/cshl_rstats_genome_scale_2023 ran into this error and I thought it was something related their laptop configurations, and for the purpose of that course, we could get around things by having them download the data from Dropbox manually.

Thanks,
Leo

[mtmorgan]

Thanks, my quasi-understanding is that this is a server misconfiguration that will presumably be fixed at some point in the future. Hopefully we can investigate more in a couple of weeks...

[mtmorgan]

I am not able to reproduce this under either Bioc-3.17 (BiocFileCache 2.8.0) or Bioc-devel (BiocFileCache 2.9.1).

Both of these have current curl, version 5.0.2, which is different from yours? There is no mention of a relevant change in news(package = "curl").

 Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.1 Patched (2023-07-17 r84704)
 os       macOS Monterey 12.6.7
 system   aarch64, darwin21.6.0
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2023-08-14
 pandoc   3.1.2 @ /Users/ma38727/homebrew/bin/pandoc

─ Packages ───────────────────────────────────────────────────────────────────
 package       * version date (UTC) lib source
 BiocFileCache   2.8.0   2023-04-25 [1] Bioconductor
 bit             4.0.5   2022-11-15 [1] CRAN (R 4.3.0)
 bit64           4.0.5   2020-08-30 [1] CRAN (R 4.3.0)
 blob            1.2.4   2023-03-17 [1] CRAN (R 4.3.0)
 cachem          1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
 cli             3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
 curl            5.0.2   2023-08-14 [1] CRAN (R 4.3.1)
...

[lcolladotor]

Interesting!

Hmmm, I just updated my curl (and other packages via BiocManager::install()) to version 5.0.2 and get the same error I was getting before. We do have some differences in our operating systems, and your R version is from about a month later than mine (though both are from R 4.3.1). I'm going to update my OS next too from Ventura 13.4 to 13.5.

library("BiocFileCache")
#> Loading required package: dbplyr
bfc <- BiocFileCache::BiocFileCache()
BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1", config = list(http_version = 2))
#> adding rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1'
#> Warning in value[[3L]](cond): 
#> trying to add rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1' produced error:
#>   HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
#> Error in BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1", : not all 'rnames' found or unique.
traceback()
#> No traceback available
options(width = 120)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.1 (2023-06-16)
#>  os       macOS Ventura 13.4
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2023-08-14
#>  pandoc   3.1.5 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package       * version date (UTC) lib source
#>  BiocFileCache * 2.8.0   2023-04-25 [1] Bioconductor
#>  bit             4.0.5   2022-11-15 [1] CRAN (R 4.3.0)
#>  bit64           4.0.5   2020-08-30 [1] CRAN (R 4.3.0)
#>  blob            1.2.4   2023-03-17 [1] CRAN (R 4.3.0)
#>  cachem          1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
#>  cli             3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
#>  curl            5.0.2   2023-08-14 [1] CRAN (R 4.3.1)
#>  DBI             1.1.3   2022-06-18 [1] CRAN (R 4.3.0)
#>  dbplyr        * 2.3.3   2023-07-07 [1] CRAN (R 4.3.0)
#>  digest          0.6.33  2023-07-07 [1] CRAN (R 4.3.0)
#>  dplyr           1.1.2   2023-04-20 [1] CRAN (R 4.3.0)
#>  evaluate        0.21    2023-05-05 [1] CRAN (R 4.3.0)
#>  fansi           1.0.4   2023-01-22 [1] CRAN (R 4.3.0)
#>  fastmap         1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
#>  filelock        1.0.2   2018-10-05 [1] CRAN (R 4.3.0)
#>  fs              1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
#>  generics        0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
#>  glue            1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
#>  htmltools       0.5.6   2023-08-10 [1] CRAN (R 4.3.0)
#>  httr            1.4.6   2023-05-08 [1] CRAN (R 4.3.0)
#>  knitr           1.43    2023-05-25 [1] CRAN (R 4.3.0)
#>  lifecycle       1.0.3   2022-10-07 [1] CRAN (R 4.3.0)
#>  magrittr        2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>  memoise         2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
#>  pillar          1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>  pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  purrr           1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
#>  R.cache         0.16.0  2022-07-21 [1] CRAN (R 4.3.0)
#>  R.methodsS3     1.8.2   2022-06-13 [1] CRAN (R 4.3.0)
#>  R.oo            1.25.0  2022-06-12 [1] CRAN (R 4.3.0)
#>  R.utils         2.12.2  2022-11-11 [1] CRAN (R 4.3.0)
#>  R6              2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  reprex          2.0.2   2022-08-17 [1] CRAN (R 4.3.0)
#>  rlang           1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
#>  rmarkdown       2.24    2023-08-14 [1] CRAN (R 4.3.1)
#>  RSQLite         2.3.1   2023-04-03 [1] CRAN (R 4.3.0)
#>  rstudioapi      0.15.0  2023-07-07 [1] CRAN (R 4.3.0)
#>  sessioninfo     1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>  styler          1.10.1  2023-06-05 [1] CRAN (R 4.3.0)
#>  tibble          3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tidyselect      1.2.0   2022-10-10 [1] CRAN (R 4.3.0)
#>  utf8            1.2.3   2023-01-31 [1] CRAN (R 4.3.0)
#>  vctrs           0.6.3   2023-06-14 [1] CRAN (R 4.3.0)
#>  withr           2.5.0   2022-03-03 [1] CRAN (R 4.3.0)
#>  xfun            0.40    2023-08-09 [1] CRAN (R 4.3.0)
#>  yaml            2.3.7   2023-01-23 [1] CRAN (R 4.3.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

^{Created on 2023-08-14 with reprex v2.0.2}

[lcolladotor]

Updating my operating system did the trick! Thanks for trying to reproduce the issue and for your companion session info!

I'm going to close the issue, but feel free to re-open it if you want. Like on the R side, I'm not sure what else could be done. Hm.... maybe using a tryCatch() chunk to detect if you are getting this type of error then checking the operating system version seems like too much of an edit for something that hopefully won't be a frequent issue. But well, maybe you have other thoughts on whether to address this from R or not.

library("BiocFileCache")
#> Loading required package: dbplyr
bfc <- BiocFileCache::BiocFileCache()
BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1", config = list(http_version = 2))
#>                                                                                                                          BFC11 
#> "/Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/147b3e65d5b8_modeling_results_BayesSpace_k09.Rdata%3Fdl%3D1"
traceback()
#> No traceback available
options(width = 120)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.1 (2023-06-16)
#>  os       macOS Ventura 13.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2023-08-14
#>  pandoc   3.1.5 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package       * version date (UTC) lib source
#>  BiocFileCache * 2.8.0   2023-04-25 [1] Bioconductor
#>  bit             4.0.5   2022-11-15 [1] CRAN (R 4.3.0)
#>  bit64           4.0.5   2020-08-30 [1] CRAN (R 4.3.0)
#>  blob            1.2.4   2023-03-17 [1] CRAN (R 4.3.0)
#>  cachem          1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
#>  cli             3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
#>  curl            5.0.2   2023-08-14 [1] CRAN (R 4.3.1)
#>  DBI             1.1.3   2022-06-18 [1] CRAN (R 4.3.0)
#>  dbplyr        * 2.3.3   2023-07-07 [1] CRAN (R 4.3.0)
#>  digest          0.6.33  2023-07-07 [1] CRAN (R 4.3.0)
#>  dplyr           1.1.2   2023-04-20 [1] CRAN (R 4.3.0)
#>  evaluate        0.21    2023-05-05 [1] CRAN (R 4.3.0)
#>  fansi           1.0.4   2023-01-22 [1] CRAN (R 4.3.0)
#>  fastmap         1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
#>  filelock        1.0.2   2018-10-05 [1] CRAN (R 4.3.0)
#>  fs              1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
#>  generics        0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
#>  glue            1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
#>  htmltools       0.5.6   2023-08-10 [1] CRAN (R 4.3.0)
#>  httr            1.4.6   2023-05-08 [1] CRAN (R 4.3.0)
#>  knitr           1.43    2023-05-25 [1] CRAN (R 4.3.0)
#>  lifecycle       1.0.3   2022-10-07 [1] CRAN (R 4.3.0)
#>  magrittr        2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>  memoise         2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
#>  pillar          1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>  pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  purrr           1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
#>  R.cache         0.16.0  2022-07-21 [1] CRAN (R 4.3.0)
#>  R.methodsS3     1.8.2   2022-06-13 [1] CRAN (R 4.3.0)
#>  R.oo            1.25.0  2022-06-12 [1] CRAN (R 4.3.0)
#>  R.utils         2.12.2  2022-11-11 [1] CRAN (R 4.3.0)
#>  R6              2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  reprex          2.0.2   2022-08-17 [1] CRAN (R 4.3.0)
#>  rlang           1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
#>  rmarkdown       2.24    2023-08-14 [1] CRAN (R 4.3.1)
#>  RSQLite         2.3.1   2023-04-03 [1] CRAN (R 4.3.0)
#>  rstudioapi      0.15.0  2023-07-07 [1] CRAN (R 4.3.0)
#>  sessioninfo     1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>  styler          1.10.1  2023-06-05 [1] CRAN (R 4.3.0)
#>  tibble          3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tidyselect      1.2.0   2022-10-10 [1] CRAN (R 4.3.0)
#>  utf8            1.2.3   2023-01-31 [1] CRAN (R 4.3.0)
#>  vctrs           0.6.3   2023-06-14 [1] CRAN (R 4.3.0)
#>  withr           2.5.0   2022-03-03 [1] CRAN (R 4.3.0)
#>  xfun            0.40    2023-08-09 [1] CRAN (R 4.3.0)
#>  yaml            2.3.7   2023-01-23 [1] CRAN (R 4.3.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

^{Created on 2023-08-14 with reprex v2.0.2}

[LiNk-NY]

FWIW I was not able to reproduce this on Monterey 12.6.8 Mac with Bioc 3.18 (even with curl 5.0.1):

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.1 (2023-06-16)
 os       macOS Monterey 12.6.8
 system   x86_64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2023-08-14
 rstudio  2023.06.1+524 Mountain Hydrangea (desktop)
 pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────
 ! package       * version   date (UTC) lib source
   Biobase         2.61.0    2023-04-25 [1] Bioconductor
   BiocAddins      0.99.18   2023-07-13 [1] Github (Bioconductor/BiocAddins@4dcd686)
   BiocBaseUtils   1.3.2     2023-07-18 [1] Bioconductor
 P BiocCheck     * 1.37.7    2023-07-17 [?] Bioconductor
   BiocFileCache * 2.9.1     2023-07-12 [1] Bioconductor
   BiocGenerics    0.47.0    2023-04-25 [1] Bioconductor
   BiocManager     1.30.22   2023-08-06 [1] local
   biocViews       1.69.1    2023-05-10 [1] Bioconductor
   bit             4.0.5     2022-11-15 [1] CRAN (R 4.3.0)
   bit64           4.0.5     2020-08-30 [1] CRAN (R 4.3.0)
   bitops          1.0-7     2021-04-24 [1] CRAN (R 4.3.0)
   blob            1.2.4     2023-03-17 [1] CRAN (R 4.3.0)
   brio            1.1.3     2021-11-30 [1] CRAN (R 4.3.0)
   cachem          1.0.8     2023-05-01 [1] CRAN (R 4.3.0)
   callr           3.7.3     2022-11-02 [1] CRAN (R 4.3.0)
   cli             3.6.1     2023-03-23 [1] CRAN (R 4.3.0)
   codetools       0.2-19    2023-02-01 [2] CRAN (R 4.3.1)
   colorout      * 1.2-2     2019-11-14 [1] Github (jalvesaq/colorout@641ed38)
   crayon          1.5.2     2022-09-29 [1] CRAN (R 4.3.0)
   curl            5.0.1     2023-06-07 [1] CRAN (R 4.3.0)

[lcolladotor]

Thanks for the info Marcel!

[lcolladotor]

Hi,

This issue has resurfaced. Unlike last time, I'm using the latest version of macOS available for my computer: macOS Sonoma 14.5 (23F79).

Have you seen this issue too?

Best,
Leo

R 4.4.0 - bioc 3.19 output

Details

library("BiocFileCache")
#> Loading required package: dbplyr

bfc <- BiocFileCache::BiocFileCache()
BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
#> adding rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1'
#> Warning in value[[3L]](cond): 
#> trying to add rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1' produced error:
#>   HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
#> Error in BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1"): not all 'rnames' found or unique.

traceback()
#> No traceback available

options(width = 120)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.0 (2024-04-24)
#>  os       macOS Sonoma 14.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2024-05-20
#>  pandoc   3.1.12.1 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package       * version date (UTC) lib source
#>  BiocFileCache * 2.12.0  2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#>  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)
#>  blob            1.2.4   2023-03-17 [1] CRAN (R 4.4.0)
#>  cachem          1.1.0   2024-05-16 [1] CRAN (R 4.4.0)
#>  cli             3.6.2   2023-12-11 [1] CRAN (R 4.4.0)
#>  curl            5.2.1   2024-03-01 [1] CRAN (R 4.4.0)
#>  DBI             1.2.2   2024-02-16 [1] CRAN (R 4.4.0)
#>  dbplyr        * 2.5.0   2024-03-19 [1] CRAN (R 4.4.0)
#>  digest          0.6.35  2024-03-11 [1] CRAN (R 4.4.0)
#>  dplyr           1.1.4   2023-11-17 [1] CRAN (R 4.4.0)
#>  evaluate        0.23    2023-11-01 [1] CRAN (R 4.4.0)
#>  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)
#>  fs              1.6.4   2024-04-25 [1] CRAN (R 4.4.0)
#>  generics        0.1.3   2022-07-05 [1] CRAN (R 4.4.0)
#>  glue            1.7.0   2024-01-09 [1] CRAN (R 4.4.0)
#>  htmltools       0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#>  httr            1.4.7   2023-08-15 [1] CRAN (R 4.4.0)
#>  knitr           1.46    2024-04-06 [1] CRAN (R 4.4.0)
#>  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)
#>  memoise         2.0.1   2021-11-26 [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)
#>  purrr           1.0.2   2023-08-10 [1] CRAN (R 4.4.0)
#>  R.cache         0.16.0  2022-07-21 [1] CRAN (R 4.4.0)
#>  R.methodsS3     1.8.2   2022-06-13 [1] CRAN (R 4.4.0)
#>  R.oo            1.26.0  2024-01-24 [1] CRAN (R 4.4.0)
#>  R.utils         2.12.3  2023-11-18 [1] CRAN (R 4.4.0)
#>  R6              2.5.1   2021-08-19 [1] CRAN (R 4.4.0)
#>  reprex          2.1.0   2024-01-11 [1] CRAN (R 4.4.0)
#>  rlang           1.1.3   2024-01-10 [1] CRAN (R 4.4.0)
#>  rmarkdown       2.27    2024-05-17 [1] CRAN (R 4.4.0)
#>  RSQLite         2.3.6   2024-03-31 [1] CRAN (R 4.4.0)
#>  sessioninfo     1.2.2   2021-12-06 [1] CRAN (R 4.4.0)
#>  styler          1.10.3  2024-04-07 [1] CRAN (R 4.4.0)
#>  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)
#>  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)
#>  xfun            0.44    2024-05-15 [1] CRAN (R 4.4.0)
#>  yaml            2.3.8   2023-12-11 [1] CRAN (R 4.4.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

^{Created on 2024-05-20 with reprex v2.1.0}

R 4.3.2 - bioc 3.18 output

Details

library("BiocFileCache")
#> Warning: package 'BiocFileCache' was built under R version 4.3.3
#> Loading required package: dbplyr

bfc <- BiocFileCache::BiocFileCache()
BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
#> adding rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1'
#> Warning in value[[3L]](cond): 
#> trying to add rname 'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1' produced error:
#>   HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
#> Error in BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1"): not all 'rnames' found or unique.

traceback()
#> No traceback available

options(width = 120)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.2 (2023-10-31)
#>  os       macOS Sonoma 14.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2024-05-20
#>  pandoc   3.1.12.1 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package       * version date (UTC) lib source
#>  BiocFileCache * 2.10.2  2024-03-30 [1] Bioconductor 3.18 (R 4.3.3)
#>  bit             4.0.5   2022-11-15 [1] CRAN (R 4.3.0)
#>  bit64           4.0.5   2020-08-30 [1] CRAN (R 4.3.0)
#>  blob            1.2.4   2023-03-17 [1] CRAN (R 4.3.0)
#>  cachem          1.1.0   2024-05-16 [1] CRAN (R 4.3.3)
#>  cli             3.6.2   2023-12-11 [1] CRAN (R 4.3.1)
#>  curl            5.2.1   2024-03-01 [1] CRAN (R 4.3.1)
#>  DBI             1.2.2   2024-02-16 [1] CRAN (R 4.3.1)
#>  dbplyr        * 2.5.0   2024-03-19 [1] CRAN (R 4.3.1)
#>  digest          0.6.35  2024-03-11 [1] CRAN (R 4.3.1)
#>  dplyr           1.1.4   2023-11-17 [1] CRAN (R 4.3.1)
#>  evaluate        0.23    2023-11-01 [1] CRAN (R 4.3.1)
#>  fansi           1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
#>  fastmap         1.2.0   2024-05-15 [1] CRAN (R 4.3.3)
#>  filelock        1.0.3   2023-12-11 [1] CRAN (R 4.3.1)
#>  fs              1.6.4   2024-04-25 [1] CRAN (R 4.3.1)
#>  generics        0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
#>  glue            1.7.0   2024-01-09 [1] CRAN (R 4.3.1)
#>  htmltools       0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
#>  httr            1.4.7   2023-08-15 [1] CRAN (R 4.3.0)
#>  knitr           1.46    2024-04-06 [1] CRAN (R 4.3.2)
#>  lifecycle       1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
#>  magrittr        2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>  memoise         2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
#>  pillar          1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>  pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  purrr           1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
#>  R.cache         0.16.0  2022-07-21 [1] CRAN (R 4.3.0)
#>  R.methodsS3     1.8.2   2022-06-13 [1] CRAN (R 4.3.0)
#>  R.oo            1.26.0  2024-01-24 [1] CRAN (R 4.3.1)
#>  R.utils         2.12.3  2023-11-18 [1] CRAN (R 4.3.1)
#>  R6              2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  reprex          2.1.0   2024-01-11 [1] CRAN (R 4.3.1)
#>  rlang           1.1.3   2024-01-10 [1] CRAN (R 4.3.1)
#>  rmarkdown       2.27    2024-05-17 [1] CRAN (R 4.3.3)
#>  RSQLite         2.3.6   2024-03-31 [1] CRAN (R 4.3.1)
#>  sessioninfo     1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>  styler          1.10.3  2024-04-07 [1] CRAN (R 4.3.1)
#>  tibble          3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tidyselect      1.2.1   2024-03-11 [1] CRAN (R 4.3.1)
#>  utf8            1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
#>  vctrs           0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
#>  withr           3.0.0   2024-01-16 [1] CRAN (R 4.3.1)
#>  xfun            0.44    2024-05-15 [1] CRAN (R 4.3.3)
#>  yaml            2.3.8   2023-12-11 [1] CRAN (R 4.3.1)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

^{Created on 2024-05-20 with reprex v2.1.0}

I've also tried with R 4.4.0 and install.packages("curl", type = "source").

[lcolladotor]

If it helps, note that this does work:

local_file <-
    tempfile("modeling_results_BayesSpace_k09.Rdata")
download.file(
    "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1",
    local_file,
    mode = "wb"
)
tools::md5sum(local_file)
#> /var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpiNWpyE/modeling_results_BayesSpace_k09.Rdatad2784a52363e 
#>                                                                             "ab6b6730efe4aeae2d79edec93ba4702"

load(local_file, verbose = TRUE)
#> Loading objects:
#>   modeling_results

options(width = 120)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.0 (2024-04-24)
#>  os       macOS Sonoma 14.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2024-05-20
#>  pandoc   3.1.12.1 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  cli           3.6.2   2023-12-11 [1] CRAN (R 4.4.0)
#>  digest        0.6.35  2024-03-11 [1] CRAN (R 4.4.0)
#>  evaluate      0.23    2023-11-01 [1] CRAN (R 4.4.0)
#>  fastmap       1.2.0   2024-05-15 [1] CRAN (R 4.4.0)
#>  fs            1.6.4   2024-04-25 [1] CRAN (R 4.4.0)
#>  glue          1.7.0   2024-01-09 [1] CRAN (R 4.4.0)
#>  htmltools     0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#>  knitr         1.46    2024-04-06 [1] CRAN (R 4.4.0)
#>  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)
#>  purrr         1.0.2   2023-08-10 [1] CRAN (R 4.4.0)
#>  R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.4.0)
#>  R.methodsS3   1.8.2   2022-06-13 [1] CRAN (R 4.4.0)
#>  R.oo          1.26.0  2024-01-24 [1] CRAN (R 4.4.0)
#>  R.utils       2.12.3  2023-11-18 [1] CRAN (R 4.4.0)
#>  reprex        2.1.0   2024-01-11 [1] CRAN (R 4.4.0)
#>  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.4.0)
#>  rmarkdown     2.27    2024-05-17 [1] CRAN (R 4.4.0)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.4.0)
#>  styler        1.10.3  2024-04-07 [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)
#>  xfun          0.44    2024-05-15 [1] CRAN (R 4.4.0)
#>  yaml          2.3.8   2023-12-11 [1] CRAN (R 4.4.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

^{Created on 2024-05-20 with reprex v2.1.0}

The above code is based on LieberInstitute/spatialLIBD#73 (comment) and it's the workaround I provide to people when they can't use spatialLIBD::fetch_data() (which internally uses BiocFileCache).

[lcolladotor]

Note that this also works:

local_file <-
    tempfile("modeling_results_BayesSpace_k09.Rdata")
curl::curl_download("http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1", destfile = local_file)
tools::md5sum(local_file)
#> /var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp9yEf2g/modeling_results_BayesSpace_k09.Rdatad6b914231bc9 
#>                                                                             "ab6b6730efe4aeae2d79edec93ba4702"

load(local_file, verbose = TRUE)
#> Loading objects:
#>   modeling_results

options(width = 120)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.0 (2024-04-24)
#>  os       macOS Sonoma 14.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2024-05-20
#>  pandoc   3.1.12.1 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  cli           3.6.2   2023-12-11 [1] CRAN (R 4.4.0)
#>  curl          5.2.1   2024-03-01 [1] CRAN (R 4.4.0)
#>  digest        0.6.35  2024-03-11 [1] CRAN (R 4.4.0)
#>  evaluate      0.23    2023-11-01 [1] CRAN (R 4.4.0)
#>  fastmap       1.2.0   2024-05-15 [1] CRAN (R 4.4.0)
#>  fs            1.6.4   2024-04-25 [1] CRAN (R 4.4.0)
#>  glue          1.7.0   2024-01-09 [1] CRAN (R 4.4.0)
#>  htmltools     0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#>  knitr         1.46    2024-04-06 [1] CRAN (R 4.4.0)
#>  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)
#>  purrr         1.0.2   2023-08-10 [1] CRAN (R 4.4.0)
#>  R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.4.0)
#>  R.methodsS3   1.8.2   2022-06-13 [1] CRAN (R 4.4.0)
#>  R.oo          1.26.0  2024-01-24 [1] CRAN (R 4.4.0)
#>  R.utils       2.12.3  2023-11-18 [1] CRAN (R 4.4.0)
#>  reprex        2.1.0   2024-01-11 [1] CRAN (R 4.4.0)
#>  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.4.0)
#>  rmarkdown     2.27    2024-05-17 [1] CRAN (R 4.4.0)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.4.0)
#>  styler        1.10.3  2024-04-07 [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)
#>  xfun          0.44    2024-05-15 [1] CRAN (R 4.4.0)
#>  yaml          2.3.8   2023-12-11 [1] CRAN (R 4.4.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

^{Created on 2024-05-20 with reprex v2.1.0}

I tried that after looking at jeroen/curl#338.