Update from httr to httr2

[lshep]

self description

[HenrikBengtsson]

To install the patch in PR #57, use:

remotes::install_github("Bioconductor/BiocFileCache#57")
packageVersion("BiocFileCache")
#> [1] '2.15.4'

To test, use:

library(BiocFileCache)
path <- tempfile()
bfc <- BiocFileCache(path, ask = FALSE)
remoteresource <- "https://bioconductorhubs.blob.core.windows.net/annotationhub/goldenpath/hg19/database/stsMap_0.0.1.RData"

## Get HTTPS proxy settings from established environment variable
proxy <- Sys.getenv("https_proxy")

## Alternatively, set it manually
proxy <- Sys.getenv("https://proxyserver:8080")

stopifnot(nzchar(proxy))
bfcadd(bfc, rname = "uniquename", fpath = remoteresource, proxy = proxy)

[HenrikBengtsson]

Environment variable https_proxy is an established variable that most internet libraries recognizes. Many systems relying on a proxy server have this set by default. Because of this, I will test both with and without that one being set.

I'll be testing with R 4.4.2 running on Rocky 8 Linux. All CRAN and Bioconductor packages are up-to-date. I'm testing with:

• BiocFileCache 2.14.0
• BiocFileCache 2.15.4 (PR Convert to httr2 #57)

installed using

BiocManager::install("BiocFileCache")
packageVersion("BiocFileCache")
#> [1] '2.14.0'

and

remotes::install_github("Bioconductor/BiocFileCache#57")
packageVersion("BiocFileCache")
#> [1] '2.15.4'

Results

Without proxy argument, without env var https_proxy

BiocFileCache 2.14.0 (ERROR)

> packageVersion("BiocFileCache")
[1] '2.14.0'
> stopifnot(!nzchar(Sys.getenv("https_proxy")))
> bfcadd(bfc, rname = "uniquename", fpath = remoteresource)
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : 
  bfcadd() failed; see warnings()
In addition: Warning messages:
1: download failed
  web resource path: 'https://bioconductorhubs.blob.core.windows.net/annotationhub/goldenpath/hg19/database/stsMap_0.0.1.RData'
  local file path: '/scratch/hb/Rtmpb7dsek/file33d16f77c6f2db/33d16f457610ee_stsMap_0.0.1.RData'
  reason: Couldn't resolve host name [bioconductorhubs.blob.core.windows.net]: Could not resolve host: bioconductorhubs.blob.core.windows.net 
2: bfcadd() failed; resource removed
  rid: BFC1
  fpath: 'https://bioconductorhubs.blob.core.windows.net/annotationhub/goldenpath/hg19/database/stsMap_0.0.1.RData'
  reason: download failed 

Enter a frame number, or 0 to exit   

1: bfcadd(bfc, rname = "uniquename", fpath = remoteresource)
2: bfcadd(bfc, rname = "uniquename", fpath = remoteresource)
3: .util_download(x, rid[i], proxy, config, "bfcadd()", ...)
4: stop(call, " failed; see warnings()")

BiocFileCache 2.15.4 (ERROR)

> packageVersion("BiocFileCache")
[1] '2.15.4'
> stopifnot(!nzchar(Sys.getenv("https_proxy")))
> bfcadd(bfc, rname = "uniquename", fpath = remoteresource)
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : 
  bfcadd() failed; see warnings()
In addition: Warning messages:
1: download failed
  web resource path: 'https://bioconductorhubs.blob.core.windows.net/annotationhub/goldenpath/hg19/database/stsMap_0.0.1.RData'
  local file path: '/scratch/hb/RtmpTQQFhC/filec3a2cb98018d/c3a2c16abc8b9_stsMap_0.0.1.RData'
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Couldn't resolve host name [bioconductorhubs.blob.core.windows.net]: Could not resolve host: bioconductorhubs.blob.core.windows.net 
2: bfcadd() failed; resource removed
  rid: BFC1
  fpath: 'https://bioconductorhubs.blob.core.windows.net/annotationhub/goldenpath/hg19/database/stsMap_0.0.1.RData'
  reason: download failed 

With proxy argument, without env var https_proxy

BiocFileCache 2.14.0 (ERROR)

> packageVersion("BiocFileCache")
[1] '2.14.0'
> stopifnot(!nzchar(Sys.getenv("https_proxy")))
> proxy <- "http://prox1:3128/"
> bfcadd(bfc, rname = "uniquename", fpath = remoteresource, proxy = proxy)
  |======================================================================| 100%

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Couldn't resolve host name [bioconductorhubs.blob.core.windows.net]: Could not resolve host: bioconductorhubs.blob.core.windows.net

Enter a frame number, or 0 to exit   

 1: bfcadd(bfc, rname = "uniquename", fpath = remoteresource, proxy = proxy)
 2: bfcadd(bfc, rname = "uniquename", fpath = remoteresource, proxy = proxy)
 3: .util_download(x, rid[i], proxy, config, "bfcadd()", ...)
 4: .util_set_cache_info(bfc, rid[ok])
 5: .httr_get_cache_info(fpath)
 6: withCallingHandlers({
    HEAD(link)
}, warning = function(w) {
    invokeRest
 7: HEAD(link)
 8: request_perform(req, hu$handle$handle)
 9: request_fetch(req$output, req$url, handle)
10: request_fetch.write_memory(req$output, req$url, handle)
11: curl::curl_fetch_memory(url, handle = handle)
12: raise_libcurl_error(6, "Couldn't resolve host name", "Could not resolve hos
13: stop(e)

BiocFileCache 2.15.4 (ERROR)

> packageVersion("BiocFileCache")
[1] '2.15.4'
> stopifnot(!nzchar(Sys.getenv("https_proxy")))
> proxy <- "http://prox1:3128/"
> bfcadd(bfc, rname = "uniquename", fpath = remoteresource, proxy = proxy)
  |======================================================================| 100%

Error in (function (e)  : Error while performing HEAD request

Enter a frame number, or 0 to exit   

 1: bfcadd(bfc, rname = "uniquename", fpath = remoteresource, proxy = proxy)
 2: bfcadd(bfc, rname = "uniquename", fpath = remoteresource, proxy = proxy)
 3: .util_download(x, rid[i], proxy, config, "bfcadd()", ...)
 4: .util_set_cache_info(bfc, rid[ok])
 5: .httr_get_cache_info(fpath)
 6: withCallingHandlers({
    request(link) %>% req_method("HEAD") %>% req_perfo
 7: request(link) %>% req_method("HEAD") %>% req_perform()
 8: req_perform(.)
 9: handle_resp(req, resp, error_call = error_call)
10: cnd_signal(resp)
11: signal_abort(cnd)
12: signalCondition(cnd)
13: (function (e) 
{
    stop("Error while performing HEAD request")
})(list(messa
14: stop("Error while performing HEAD request")

---

Without proxy argument, with env var https_proxy

BiocFileCache 2.14.0 (OK)

> packageVersion("BiocFileCache")
[1] '2.14.0'
> stopifnot(nzchar(Sys.getenv("https_proxy")))
> bfcadd(bfc, rname = "uniquename", fpath = remoteresource)
                                                                         BFC1 
"/scratch/hb/RtmpSntGNu/file2787ed29233941/2787ed52b68dc8_stsMap_0.0.1.RData" 

BiocFileCache 2.15.4 (OK)

> packageVersion("BiocFileCache")
[1] '2.15.4'
> stopifnot(nzchar(Sys.getenv("https_proxy")))
> bfcadd(bfc, rname = "uniquename", fpath = remoteresource)

                                                                         BFC1
"/scratch/hb/RtmpSntGNu/file2787ed6216c1cc/2787ed6e178db_stsMap_0.0.1.RData"

With proxy argument, with env var https_proxy

BiocFileCache 2.14.0 (OK)

> packageVersion("BiocFileCache")
[1] '2.14.0'
> proxy <- Sys.getenv("https_proxy")
> stopifnot(nzchar(proxy))
> bfcadd(bfc, rname = "uniquename", fpath = remoteresource, proxy = proxy)
  |======================================================================| 100%

                                                                         BFC1
"/scratch/hb/RtmpSntGNu/file27821d6216c1cc/2787ed6e178db_stsMap_0.0.1.RData"

BiocFileCache 2.15.4 (OK)

> packageVersion("BiocFileCache")
[1] '2.15.4'
> proxy <- Sys.getenv("https_proxy")
> stopifnot(nzchar(proxy))
> bfcadd(bfc, rname = "uniquename", fpath = remoteresource, proxy = proxy)
  |======================================================================| 100%

                                                                        BFC1 
"/scratch/hb/RtmpSntGNu/file2787ed6216c1cc/2787ed6e178db_stsMap_0.0.1.RData"