req_error error triggered by downloading the lun spikein 2017 data (R 4.4, curl 8.6.0, bioc 3.19)

[lcolladotor]

Hi,

During a course we ran into this issue in @xxchenm's computer:

> library("scRNAseq")
> sce.416b <- LunSpikeInData(which = "416b")
Error in save_file(path = paste(project, asset, version, x, sep = "/"),  : 
  failed to save 'scRNAseq/lun-spikein-2017/2023-12-18/..manifest'; Failed to parse error body with method defined in `req_error()`.
> traceback()
7: stop("failed to save '", path, "'; ", status)
6: save_file(path = paste(project, asset, version, x, sep = "/"), 
       destination = file.path(destination, x), overwrite = overwrite, 
       url = url)
5: FUN(X[[i]], ...)
4: lapply(listing, FUN)
3: saveVersion(package, name, version, cache = cache, overwrite = overwrite)
2: fetchDataset("lun-spikein-2017", "2023-12-18", path = which, 
       realize.assays = TRUE)
1: LunSpikeInData(which = "416b")
> 
> 
> 

I see that this student has system curl version 8.6.0, so this issue could be related to curl/curl#13725, Bioconductor/BiocFileCache#48, and related issues.

But well, maybe you know of other reasons for this issue. Note that we tried downloading this data with both legacy = TRUE and FALSE, and got the same req_error() issue.

Best,
Leo

R Session Info

Details

> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24)
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 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2024-06-11
 rstudio  2024.04.1+748 Chocolate Cosmos (desktop)
 pandoc   NA

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 [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
> curl::curl_version()
$version
[1] "8.6.0"

$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"    "https"   "imap"    "imaps"   "ldap"   
[12] "ldaps"   "mqtt"    "pop3"    "pop3s"   "rtsp"    "smb"     "smbs"    "smtp"    "smtps"   "telnet"  "tftp"   

$ipv6
[1] TRUE

$http2
[1] TRUE

$idn
[1] FALSE

[LTLA]

Smells like SingleR-inc/celldex#28.

[xxchenm]

Thanks for your suggestion. I do have the VPN, but the error still shows up after I turn it off.

Best,
Xuan

[LTLA]

Try installing the master branch of https://github.com/ArtifactDB/gypsum-R, start a new session and re-run the relevant commands. It won't fix the problem but it will at least reveal the actual error message.

[lcolladotor]

Hi @xxchenm,

Can you run the following?

BiocManager::install("ArtifactDB/gypsum-R@master")

then in a new R session run:

library("scRNAseq")
sce.416b <- LunSpikeInData(which = "416b")
traceback()

Thanks in advance!

Best,
Leo

[xxchenm]

Hi @LTLA and @lcolladotor,

I got the following error when run:

sce.416b <- LunSpikeInData(which = "416b")
Error in req_perform():
! HTTP 403 Forbidden.
•

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D22 Sorry, you don't have permission to visit this site. <style> .red {background-color:#002e6d;} .yl {background-color:#002e6d;} .bh {background-color:#002e6d;} .eu_co.st {background-color:#002e6d;} .eu_h { font-size: 0; } .eu_h i { display: none; } hr:first-of-type { display: none; } </style> Access to this site is prohibited by Mayo Clinic Policy. Access to this website is restricted on your work computer because it violates policy and/or poses a security risk to Mayo Clinic's network. If you need access to this website to complete your work, please contact the Help Desk. Not allowed to browse Gambling category You tried to visit: https://gypsum.artifactdb.com/list?prefix=scRNAseq%2Flun-spikein-2017%2F2023-12-18%2F&... See our internet use policy. Need help? Contact our support team at 507-284-5500 Your organization has selected Zscaler to protect you from internet threats.

Run `rlang::last_trace()` to see where the error occurred.

Thanks so much for your help! I appreciate it.

Best,
Xuan

[LTLA]

As you can see from the error messages, Zscaler is blocking access. It's literally the same problem as discussed in SingleR-inc/celldex#28. You'll have to get around your firewall/proxy/VPN/whatever Zscalar is doing.

The problem is that, before I bought it, the artifactdb.com domain was owned by some gambling website. I don't know how to get it taken off these blacklists from my end, so you'll have to ask your IT team to do so.

[xxchenm]

Thanks so much! I will work with our IT team on this.

Best,
Xuan