Closed lcolladotor closed 6 months ago
mtmorgan
commented
1 year ago 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
commented
1 year ago 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
commented
1 year ago 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
commented
1 year ago 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
commented
1 year ago 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)Thanks for the info Marcel!
lcolladotor
commented
6 months ago 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
I've also tried with R 4.4.0 and install.packages("curl", type = "source").
lcolladotor
commented
6 months ago 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_resultsoptions(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 https://github.com/LieberInstitute/spatialLIBD/issues/73#issuecomment-2016520542 and it's the workaround I provide to people when they can't use spatialLIBD::fetch_data() (which internally uses BiocFileCache).
lcolladotor
commented
6 months ago 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_resultsoptions(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 https://github.com/jeroen/curl/issues/338.
lcolladotor
commented
6 months ago Also this works:
websource <- "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1"
local_file <-
tempfile("modeling_results_BayesSpace_k09.Rdata")
httr::GET(websource, httr::progress(con = stderr()), config= list(),
httr::write_disk(local_file, overwrite=TRUE))
#> Response [https://ucc9233162d1f4ce89cda3dc33db.dl.dropboxusercontent.com/cd/0/get/CTQsU5KdGZ49ZnCdyfN2Vm5KaWMrGU8IW06HCAaOx4y2tFBc7NoVTgvO-pI2df3n7k840W83qcpQ-qIxqaW2sGDo2GET4s4JC0q5llXElgUU-XRrBDDpuvNfUFpsf8iL_FuH8AO3AB58hCRU4X_NxdLH/file?dl=1]
#> Date: 2024-05-20 14:02
#> Status: 200
#> Content-Type: application/binary
#> Size: 12.3 MB
#> <ON DISK> /var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpuMCdUx/modeling_results_BayesSpace_k09.Rdatad9b73f154781tools::md5sum(local_file)
#> /var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpuMCdUx/modeling_results_BayesSpace_k09.Rdatad9b73f154781
#> "ab6b6730efe4aeae2d79edec93ba4702"load(local_file, verbose = TRUE)
#> Loading objects:
#> modeling_resultsoptions(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)
#> 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)
#> 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)
#> 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
That was from adapting the internal BiocFileCache code at https://github.com/Bioconductor/BiocFileCache/blob/8458c9d0e80238ba2b9ee1bd07931822a78d4af2/R/httr.R#L62-L67. I saw that BiocFileCache:::.httr_download() gets used by BiocFileCache:::.util_download_and_rename(), which is used by bfcdownload(). But well, I can't see the connection to those functions from bfcrpath(), but maybe you do.
mtmorgan
commented
6 months ago It's more helpful to use traceback() to see where the error is occurring, followed by debug() or options(error=recover) to identify the explicit call and values that cause the problem, and finally to do the call outside the BiocFileCache framework, where you'll reproduced the error with a minimal example; currently it sounds like a curl problem rather than BiocFileCache...
Also it seems like the most helpful debuging information comes from curl::curl_version(). I have
> curl::curl_version()
$version
[1] "8.4.0"
$ssl_version
[1] "(SecureTransport) LibreSSL/3.3.6"
$libz_version
[1] "1.2.12"
$libssh_version
[1] NA
$libidn_version
[1] NA
$host
[1] "x86_64-apple-darwin23.0"
$protocols
[1] "dict" "file" "ftp" "ftps" "gopher" "gophers" "http"
[8] "https" "imap" "imaps" "ldap" "ldaps" "mqtt" "pop3"
[15] "pop3s" "rtsp" "smb" "smbs" "smtp" "smtps" "telnet"
[22] "tftp"
$ipv6
[1] TRUE
$http2
[1] TRUE
$idn
[1] FALSEand also no problems (Sonoma 14.4.1) with the command
> bfc = BiocFileCache(tempfile())
/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T//Rtmpq4qT5r/file127deb0da726
does not exist, create directory? (yes/no): yes
> 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'
|=====================================================================| 100%
BFC1
"/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T//Rtmpq4qT5r/file127deb0da726/127de2d58b575_modeling_results_BayesSpace_k09.Rdata%3Fdl%3D1"
> sessionInfo()
R version 4.4.0 beta (2024-04-14 r86424)
Platform: aarch64-apple-darwin23.4.0
Running under: macOS Sonoma 14.4.1
Matrix products: default
BLAS: /Users/ma38727/bin/R-4-4-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-4-4-branch/lib/libRlapack.dylib; LAPACK version 3.12.0
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocFileCache_2.13.0 dbplyr_2.5.0
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 httr_1.4.7 cli_3.6.2 rlang_1.1.3
[5] DBI_1.2.2 purrr_1.0.2 generics_0.1.3 glue_1.7.0
[9] bit_4.0.5 fansi_1.0.6 tibble_3.2.1 filelock_1.0.3
[13] fastmap_1.1.1 lifecycle_1.0.4 memoise_2.0.1 compiler_4.4.0
[17] dplyr_1.1.4 RSQLite_2.3.6 blob_1.2.4 pkgconfig_2.0.3
[21] R6_2.5.1 tidyselect_1.2.1 utf8_1.2.4 pillar_1.9.0
[25] curl_5.2.1 magrittr_2.0.3 withr_3.0.0 tools_4.4.0
[29] bit64_4.0.5 cachem_1.0.8
>Without being able to reproduce the error, I can only guess that the following is a minimal reproducible example
url = "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1"
path = tempfile()
handle = curl::new_handle()
curl::curl_fetch_disk(url, path, handle)Hi Martin,
curl::curl_fetch_disk() worksThanks for the smaller code. I ran it and did not run into any problems with it as shown below.
options(error = recover) outputBased on httr::GET() andcurl::curl_download() working too, I'm wondering if some info BiocFileCache expects is absent from curl with the versions I have installed.
Here's also some output with options(error=recover). My understanding is that it runs well until https://github.com/Bioconductor/BiocFileCache/blob/8458c9d0e80238ba2b9ee1bd07931822a78d4af2/R/BiocFileCache-class.R#L585 as the rmdx object does have a length > 0.
> options(error=recover)
> 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'
|======================================================================| 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)
Enter a frame number, or 0 to exit
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
Selection: 1
Called from: top level
Browse[1]> ls()
[1] "exact" "rids" "rnames" "x"
Browse[1]> ls.str()
exact : logi TRUE
rids : <missing>
rnames : chr "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1"
x : Formal class 'BiocFileCache' [package "BiocFileCache"] with 1 slot
Browse[1]> x
class: BiocFileCache
bfccache: /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache
bfccount: 0
For more information see: bfcinfo() or bfcquery()
Browse[1]> c
Enter a frame number, or 0 to exit
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
Selection: 2
Called from: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
Browse[1]> ls.str()
add_or_return_rname : function (x, rname, ..., exact)
exact : logi TRUE
rids : chr(0)
rids0 : Named chr NA
rmdx : chr "BFC11"
rnames : chr "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1"
update_time_and_path : function (x, i)
x : Formal class 'BiocFileCache' [package "BiocFileCache"] with 1 slot
Browse[1]> bfcrid(x)
character(0)
Browse[1]> rids
character(0)
Browse[1]> rids0
http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1
NA
Browse[1]> rmdx
[1] "BFC11"
Browse[1]> setdiff(bfcrid(x), rids)
character(0)
Browse[1]> bfcrpath(x, rids = rids0)
Error during wrapup: all(rids %in% bfcrid(x)) is not TRUE
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]> traceback()
No traceback available
Browse[1]> c
Enter a frame number, or 0 to exit
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
Selection: 2
Called from: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
Browse[1]> n
Enter a frame number, or 0 to exit
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
Selection: s
Enter an item from the menu, or 0 to exit
Selection: 2
Browse[1]> s
Enter a frame number, or 0 to exit
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
Selection:traceback() outputHere's also the manual traceback() output since it seems like reprex::reprex() didn't capture it:
> 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")
> 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'
|======================================================================| 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)
> traceback()
3: stop("not all 'rnames' found or unique.")
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")From there, I see that https://github.com/Bioconductor/BiocFileCache/blob/8458c9d0e80238ba2b9ee1bd07931822a78d4af2/R/BiocFileCache-class.R#L586 is being the error triggered.
Best, Leo
lcolladotor
commented
6 months ago Hi again,
Browse[1]>
Enter a frame number, or 0 to exit
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
Selection:
Enter an item from the menu, or 0 to exit
Selection: 1
Browse[1]> ls()
[1] "exact" "rids" "rnames" "x"
Browse[1]> ls.str()
exact : logi TRUE
rids : <missing>
rnames : chr "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1"
x : Formal class 'BiocFileCache' [package "BiocFileCache"] with 1 slot
Browse[1]> bfcrid(x)
character(0)
Browse[1]> rname <- rnames[1]
Browse[1]> res <- bfcrid(bfcquery(x, rname, field="rname", exact = exact))
Browse[1]> res
character(0)
Browse[1]> id <- "add_or_return_rname"
Browse[1]> locfile_path <- file.path(bfccache(x), id)
Browse[1]> locfile <- .lock2(locfile_path, exclusive = TRUE)
Browse[1]> res <- bfcrid(bfcquery(x, rname, field="rname", exact = exact))
Browse[1]> length(res)
[1] 0
Browse[1]> bfcadd(x, rname)
|======================================================================| 100%
Error during wrapup: HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
Error: no more error handlers available (recursive errors?); invoking 'abort' restartUsing the options(error=recover) mode, I went to the first option in the browser mode and ran code manually till getting to https://github.com/Bioconductor/BiocFileCache/blob/8458c9d0e80238ba2b9ee1bd07931822a78d4af2/R/BiocFileCache-class.R#L550C27-L550C42.
Then I got a new smaller reproducible example with its traceback() output:
library("BiocFileCache")
bfc <- BiocFileCache::BiocFileCache()
bfcadd(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")> library("BiocFileCache")
Loading required package: dbplyr
> bfc <- BiocFileCache::BiocFileCache()
> bfcadd(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
|======================================================================| 100%
Error in curl::curl_fetch_memory(url, handle = handle) :
HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
> traceback()
11: curl::curl_fetch_memory(url, handle = handle)
10: request_fetch.write_memory(req$output, req$url, handle)
9: request_fetch(req$output, req$url, handle)
8: request_perform(req, hu$handle$handle)
7: HEAD(link)
6: withCallingHandlers({
HEAD(link)
}, warning = function(w) {
invokeRestart("muffleWarning")
})
5: .httr_get_cache_info(fpath)
4: .util_set_cache_info(bfc, rid[ok])
3: .util_download(x, rid[i], proxy, config, "bfcadd()", ...)
2: bfcadd(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
1: bfcadd(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")Navigating that output, I got to https://github.com/Bioconductor/BiocFileCache/blob/8458c9d0e80238ba2b9ee1bd07931822a78d4af2/R/httr.R#L5, which leads to an even shorter reproducible example.
> httr::HEAD("http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
Error in curl::curl_fetch_memory(url, handle = handle) :
HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
> traceback()
5: curl::curl_fetch_memory(url, handle = handle)
4: request_fetch.write_memory(req$output, req$url, handle)
3: request_fetch(req$output, req$url, handle)
2: request_perform(req, hu$handle$handle)
1: httr::HEAD("http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")The above code does run well in a different setup (the HPC environment I have access to at work):
> httr::HEAD("http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
Response [https://uc3bfce8a204fbffc8c2c4a98fd9.dl.dropboxusercontent.com/cd/0/get/CTS2_3XITELM2KSAE_Qh46834uS63kMAoVskY_o_fWc5A2wgbjgfrpunSESznpLbLN0oSZbM1nsZcn87VMggDvQPxPnYCcXQV0RDOXFSabRrooQrtABqtcSckf9flESrxDHzDvajnP4CAILi4MOxNzoM/file?dl=1]
Date: 2024-05-20 16:36
Status: 200
Content-Type: application/json
<EMPTY BODY>
> options(width = 120)
sessioninfo::session_info()
curl::curl_version()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.2 Patched (2024-02-08 r85876)
os Rocky Linux 9.2 (Blue Onyx)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz US/Eastern
date 2024-05-20
pandoc 3.1.3 @ /jhpce/shared/community/core/conda_R/4.3.x/bin/pandoc
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cli 3.6.2 2023-12-11 [2] CRAN (R 4.3.2)
colorout * 1.3-0.1 2023-11-29 [1] Github (jalvesaq/colorout@deda341)
colorspace 2.1-0 2023-01-23 [2] CRAN (R 4.3.2)
curl 5.2.0 2023-12-08 [2] CRAN (R 4.3.2)
digest 0.6.34 2024-01-11 [2] CRAN (R 4.3.2)
dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.2)
fansi 1.0.6 2023-12-08 [2] CRAN (R 4.3.2)
fastmap 1.1.1 2023-02-24 [2] CRAN (R 4.3.2)
generics 0.1.3 2022-07-05 [2] CRAN (R 4.3.2)
ggplot2 3.4.4 2023-10-12 [2] CRAN (R 4.3.2)
glue 1.7.0 2024-01-09 [2] CRAN (R 4.3.2)
gtable 0.3.4 2023-08-21 [2] CRAN (R 4.3.2)
htmltools 0.5.7 2023-11-03 [2] CRAN (R 4.3.2)
htmlwidgets 1.6.4 2023-12-06 [2] CRAN (R 4.3.2)
httpuv 1.6.14 2024-01-26 [2] CRAN (R 4.3.2)
httr 1.4.7 2023-08-15 [2] CRAN (R 4.3.2)
jsonlite 1.8.8 2023-12-04 [2] CRAN (R 4.3.2)
later 1.3.2 2023-12-06 [2] CRAN (R 4.3.2)
lattice 0.22-5 2023-10-24 [3] CRAN (R 4.3.2)
lifecycle 1.0.4 2023-11-07 [2] CRAN (R 4.3.2)
magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.3.2)
munsell 0.5.0 2018-06-12 [2] CRAN (R 4.3.2)
pillar 1.9.0 2023-03-22 [2] CRAN (R 4.3.2)
pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.3.2)
png 0.1-8 2022-11-29 [2] CRAN (R 4.3.2)
promises 1.2.1 2023-08-10 [2] CRAN (R 4.3.2)
R6 2.5.1 2021-08-19 [2] CRAN (R 4.3.2)
Rcpp 1.0.12 2024-01-09 [2] CRAN (R 4.3.2)
rlang 1.1.3 2024-01-10 [2] CRAN (R 4.3.2)
rmote 0.3.4 2023-11-29 [1] Github (cloudyr/rmote@fbce611)
scales 1.3.0 2023-11-28 [2] CRAN (R 4.3.2)
servr 0.27 2023-05-02 [1] CRAN (R 4.3.2)
sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.3.2)
tibble 3.2.1 2023-03-20 [2] CRAN (R 4.3.2)
tidyselect 1.2.0 2022-10-10 [2] CRAN (R 4.3.2)
utf8 1.2.4 2023-10-22 [2] CRAN (R 4.3.2)
vctrs 0.6.5 2023-12-01 [2] CRAN (R 4.3.2)
xfun 0.42 2024-02-08 [2] CRAN (R 4.3.2)
[1] /users/lcollado/R/4.3.x
[2] /jhpce/shared/community/core/conda_R/4.3.x/R/lib64/R/site-library
[3] /jhpce/shared/community/core/conda_R/4.3.x/R/lib64/R/library
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
$version
[1] "8.1.2"
$ssl_version
[1] "OpenSSL/3.1.5"
$libz_version
[1] "1.2.13"
$libssh_version
[1] "libssh2/1.11.0"
$libidn_version
[1] NA
$host
[1] "x86_64-conda-linux-gnu"
$protocols
[1] "dict" "file" "ftp" "ftps" "gopher" "gophers" "http" "https" "imap" "imaps" "mqtt"
[12] "pop3" "pop3s" "rtsp" "scp" "sftp" "smb" "smbs" "smtp" "smtps" "telnet" "tftp"
$ipv6
[1] TRUE
$http2
[1] TRUE
$idn
[1] FALSE
>Best, Leo
lcolladotor
commented
6 months ago In case it's useful, here's more verbose output from httr::HEAD(). I was trying to see if the suggestion from https://github.com/jeroen/curl/issues/232#issuecomment-1231686216 would work, but it doesn't.
> httr::HEAD("http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1", config = httr::config(http_version=2, forbid_reuse=TRUE))
Error in curl::curl_fetch_memory(url, handle = handle) :
chunk hex-length char not a hex digit: 0x1f
> traceback()
5: curl::curl_fetch_memory(url, handle = handle)
4: request_fetch.write_memory(req$output, req$url, handle)
3: request_fetch(req$output, req$url, handle)
2: request_perform(req, hu$handle$handle)
1: httr::HEAD("http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1",
config = httr::config(http_version = 2, forbid_reuse = TRUE))On the HPC system I can use, it does work:
> httr::HEAD("http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1", config = httr::config(http_version=2, forbid_reuse=TRUE))
Response [https://ucd3a9ce967aa423ff53dfce3fab.dl.dropboxusercontent.com/cd/0/get/CTS8sMMFV9VT4s6vrKigycGYF3rx1eoNDFVVI0iedt5v_3qfKqK3soJqepGGiFj-LZISyaz1ibERXe1G-7buAwp_vEw1ajt5ItQLKdZSFfvbH1LHMMCewwj3MkVRTs0Sifc-RNibpc7P0Tc34lroo9dS/file?dl=1]
Date: 2024-05-20 17:23
Status: 200
Content-Type: application/json
<EMPTY BODY>I can imagine a few paths forward:
httr::HEAD() / curl::curl_fetch_memory() updates.
httr::HEAD() in BiocFileCache at https://github.com/Bioconductor/BiocFileCache/blob/8458c9d0e80238ba2b9ee1bd07931822a78d4af2/R/httr.R#L5. Other httr functions seem to be working now.
BiocFileCache).I'll think about what to do given that I'll be using some of this data for a course in a few weeks (June 9-11 https://github.com/lcolladotor/cshl_rstats_genome_scale_2024).
Best, Leo
jeroen
commented
6 months ago Reported this upstream here: https://github.com/curl/curl/issues/13725
lcolladotor
commented
6 months ago Thank you very much @jeroen!
jeroen
commented
6 months ago I think this bug is now fixed in libcurl 8.8.0 (released today!).
lcolladotor
commented
6 months ago Hi,
This bug is indeed fixed with libcurl 8.8.0. Thanks @jeroen @mtmorgan!
Here's the short version:
> httr::HEAD("http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
Response [https://ucdbc32b7b700d6261f94c3da621.dl.dropboxusercontent.com/cd/0/get/CTbe7dI6tdpq8dtOuGenty52KBo-ipktH2JhguDt2PNGBhJ5l3oAvIsfFLFpM0CV0gUXElQQrWSQVy9l879G0xoV0tkWHWLs5tIULWB8tu0YKGki7Fm_a9mdfaKKf7RbTlCnm9riOI6B7uv9Mp7Tcm-D/file?dl=1]
Date: 2024-05-22 14:01
Status: 200
Content-Type: application/json
<EMPTY BODY>Next, I show in more detailed steps I took.
Thanks again! Leo
libcurl 8.8.0curl version 8.7.1 is the one available right now from Homebrew at https://formulae.brew.sh/formula/curl. I tried brew install --HEAD curl but that didn't work.
The instructions at https://curl.se/docs/install.html for Apple systems was a bit confusing to me. The Feeling Brave? Build curl yourself! section of https://snyk.io/blog/how-to-update-curl/ helped me a bit.
From https://github.com/Homebrew/homebrew-core/blob/e15ae5d5eba1a35089f0776216e91d38d4689a4a/Formula/c/curl.rb#L5, I figured that I should download the file ending with .tar.bz2 from https://github.com/curl/curl/releases/tag/curl-8_8_0. Note that by this point, I likely already had run brew install curl pkg-config (in case this matters for reproducibility).
In the end I used this:
cd ~/Desktop
wget https://github.com/curl/curl/releases/download/curl-8_8_0/curl-8.8.0.tar.bz2
## manually uncompressed curl-8.8.0.tar.bz2 which created the curl-8.8.0 directory
cd curl-8.8.0
## I copied the instructions from https://curl.se/docs/install.html
## then edited the ARCH and DEPLOYMENT_TARGET variables
export ARCH=arm64
export SDK=macosx
export DEPLOYMENT_TARGET=14.5
export CFLAGS="-arch $ARCH -isysroot $(xcrun -sdk $SDK --show-sdk-path) -m$SDK-version-min=$DEPLOYMENT_TARGET"
./configure --host=$ARCH-apple-darwin --prefix $(pwd)/artifacts --with-secure-transport
make -j8
make installI then re-compiled curl in R by adapting the instructions from https://github.com/jeroen/curl?tab=readme-ov-file#macos-using-curl-from-homebrew. I didn't have to edit my PATH variable on my ~/.zshrc file to get this to work.
> Sys.setenv(PKG_CONFIG_PATH="/Users/leocollado/Desktop/curl-8.8.0/artifacts/lib/pkgconfig")
> install.packages("curl", type = "source")
trying URL 'https://cloud.r-project.org/src/contrib/curl_5.2.1.tar.gz'
Content type 'application/x-gzip' length 716695 bytes (699 KB)
==================================================
downloaded 699 KB
Loading required package: colorout
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include
Using PKG_LIBS=-L/Users/leocollado/Desktop/curl-8.8.0/artifacts/lib -lcurl
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using SDK: ‘MacOSX14.4.sdk’
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c callbacks.c -o callbacks.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c curl.c -o curl.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c download.c -o download.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c escape.c -o escape.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fetch.c -o fetch.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findport.c -o findport.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c form.c -o form.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getdate.c -o getdate.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c handle.c -o handle.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ieproxy.c -o ieproxy.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interrupt.c -o interrupt.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multi.c -o multi.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nslookup.c -o nslookup.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c options.c -o options.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c reflist.c -o reflist.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c split.c -o split.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ssl.c -o ssl.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c typechecking.c -o typechecking.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c version.c -o version.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c winidn.c -o winidn.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/leocollado/Desktop/curl-8.8.0/artifacts/include -DSTRICT_R_HEADERS -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c writer.c -o writer.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -L/Users/leocollado/Desktop/curl-8.8.0/artifacts/lib -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-curl/00new/curl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Loading required package: colorout
** help
*** installing help indices
** building package indices
Loading required package: colorout
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: colorout
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Loading required package: colorout
** testing if installed package keeps a record of temporary installation path
* DONE (curl)
The downloaded source packages are in
‘/private/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T/Rtmp2jZmXO/downloaded_packages’I verified that the output of curl::curl_version() listed version 8.8.0.
> curl::curl_version()
$version
[1] "8.8.0"
$ssl_version
[1] "SecureTransport"
$libz_version
[1] "1.2.12"
$libssh_version
[1] NA
$libidn_version
[1] "2.3.7"
$host
[1] "aarch64-apple-darwin"
$protocols
[1] "dict" "file" "ftp" "ftps" "gopher" "gophers" "http"
[8] "https" "imap" "imaps" "ldap" "ldaps" "mqtt" "pop3"
[15] "pop3s" "rtsp" "smb" "smbs" "smtp" "smtps" "telnet"
[22] "tftp"
$ipv6
[1] TRUE
$http2
[1] TRUE
$idn
[1] TRUEThe smaller test worked immediately.
> httr::HEAD("http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
Response [https://ucdbc32b7b700d6261f94c3da621.dl.dropboxusercontent.com/cd/0/get/CTbe7dI6tdpq8dtOuGenty52KBo-ipktH2JhguDt2PNGBhJ5l3oAvIsfFLFpM0CV0gUXElQQrWSQVy9l879G0xoV0tkWHWLs5tIULWB8tu0YKGki7Fm_a9mdfaKKf7RbTlCnm9riOI6B7uv9Mp7Tcm-D/file?dl=1]
Date: 2024-05-22 14:01
Status: 200
Content-Type: application/json
<EMPTY BODY>But my BiocFileCache::bfcrpath() failed with a different error message suggesting that I should use bfcquery().
> 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")
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 FUN(X[[i]], ...) : 'rnames' exact pattern
'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1'
is not unique; use 'bfcquery()' to see matches.
> traceback()
3: stop("not all 'rnames' found or unique.")
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
I however initially just tried the earlier bfcadd() example, which worked.
> bfcadd(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
|======================================================================| 100%
BFC18
"/Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/23a11ed998ca_modeling_results_BayesSpace_k09.Rdata%3Fdl%3D1"I then tried some of the options(error=recover) code from earlier. There I noticed in particular this piece:
> bfcrid(x)
[1] "BFC15" "BFC16" "BFC17" "BFC18"> BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=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.
In addition: Warning message:
In FUN(X[[i]], ...) : 'rnames' exact pattern
'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1'
is not unique; use 'bfcquery()' to see matches.
> options(error=recover)
> BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=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.
In addition: Warning message:
In FUN(X[[i]], ...) : 'rnames' exact pattern
'http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1'
is not unique; use 'bfcquery()' to see matches.
Enter a frame number, or 0 to exit
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
Selection: 1
Called from: top level
Browse[1]> ls.str()
exact : logi TRUE
rids : <missing>
rnames : chr "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1"
x : Formal class 'BiocFileCache' [package "BiocFileCache"] with 1 slot
Browse[1]> bfcrid(x)
[1] "BFC15" "BFC16" "BFC17" "BFC18"
Browse[1]> n
Enter a frame number, or 0 to exit
1: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
2: BiocFileCache::bfcrpath(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/mode
Selection: 0
I then tried using bfcquery() which I didn't remember the syntax for. Some of the info at https://bioconductor.org/packages/release/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#investigating-accessing-resources was useful to remember this.
> bfcquery()
... exact= field= query= x=
> bfcquery(query = "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1", x = bfc)
# A tibble: 0 × 10
# ℹ 10 variables: rid <chr>, rname <chr>, create_time <dbl>, access_time <dbl>,
# rpath <chr>, rtype <chr>, fpath <chr>, last_modified_time <dbl>,
# etag <chr>, expires <dbl>
> bfcquery(bfc, "http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1")
# A tibble: 0 × 10
# ℹ 10 variables: rid <chr>, rname <chr>, create_time <dbl>, access_time <dbl>,
# rpath <chr>, rtype <chr>, fpath <chr>, last_modified_time <dbl>,
# etag <chr>, expires <dbl>But well, I wasn't being able to find the IDs that I had already found earlier under options(error=recover). So I then simply removed them with bfcremove(), and after cleaning up my BiocFileCache from earlier attempts to download http://www.dropbox.com/s/srkb2ife75px2yz/modeling_results_BayesSpace_k09.Rdata?dl=1, things worked well ^^.
> bfcremove(bfc, c("BFC15", "BFC16", "BFC17", "BFC18"))
> 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'
|======================================================================| 100%
BFC19
"/Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/23a134616f43_modeling_results_BayesSpace_k09.Rdata%3Fdl%3D1"Here's the R session info
> 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 2024-05-22
pandoc 3.2 @ /opt/homebrew/bin/pandoc
─ 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)
brio 1.1.5 2024-04-24 [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)
colorout * 1.3-0.2 2024-05-03 [1] Github (jalvesaq/colorout@c6113a2)
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)
devtools * 2.4.5 2022-10-11 [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)
ellipsis 0.3.2 2021-04-29 [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)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0)
later 1.3.2 2023-12-06 [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)
mime 0.12 2021-09-28 [1] CRAN (R 4.4.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.4.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.4.0)
promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0)
prompt 1.0.2.9000 2024-05-03 [1] Github (gaborcsardi/prompt@17bd0e1)
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)
Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.0)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0)
RSQLite 2.3.6 2024-03-31 [1] CRAN (R 4.4.0)
rsthemes 0.4.0 2024-05-03 [1] Github (gadenbuie/rsthemes@34a55a4)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0)
stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0)
stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
testthat * 3.2.1.1 2024-04-14 [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)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.0)
usethis * 2.2.3 2024-02-19 [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)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0)
[1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
>
> curl::curl_version()
$version
[1] "8.8.0"
$ssl_version
[1] "SecureTransport"
$libz_version
[1] "1.2.12"
$libssh_version
[1] NA
$libidn_version
[1] "2.3.7"
$host
[1] "aarch64-apple-darwin"
$protocols
[1] "dict" "file" "ftp" "ftps" "gopher" "gophers" "http" "https" "imap" "imaps" "ldap"
[12] "ldaps" "mqtt" "pop3" "pop3s" "rtsp" "smb" "smbs" "smtp" "smtps" "telnet" "tftp"
$ipv6
[1] TRUE
$http2
[1] TRUE
$idn
[1] TRUE
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 areprexbelow abstracting away thespatialLIBDlayer.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
biocthisworkflow as well as in the Bioconductor BBS system.In the 30 min prior to our
spatialLIBDBioC2023 demo with @lahuuki, I tried resolving this. By googling the error message, I realized thatcurl(andhttr),BiocFileCachedependencies, now use http version 2 instead of 1.1. See https://github.com/jeroen/curl/issues/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 aBiocFileCacheuser. Maybe through theconfigargument https://github.com/search?q=repo%3ABioconductor%2FBiocFileCache%20config&type=code. But that doesn't seem to be the case (maybe I'm not specifyingconfigwhere I should):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