##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scp
###
##############################################################################
##############################################################################


* checking for file ‘scp/DESCRIPTION’ ... OK
* preparing ‘scp’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘QFeatures_nutshell.Rmd’ using rmarkdown
2025-10-26 17:54:27.329 R[80926:551218014] XType: Using static font registry.
[WARNING] Could not fetch resource https://rformassspectrometry.github.io/QFeatures/articles/QFeatures_files/figure-html/featuresplot-1.png: HttpExceptionRequest Request {
    host                 = "rformassspectrometry.github.io"
    port                 = 443
    secure               = True
    requestHeaders       = []
    path                 = "/QFeatures/articles/QFeatures_files/figure-html/featuresplot-1.png"
    queryString          = ""
    method               = "GET"
    proxy                = Nothing
    rawBody              = False
    redirectCount        = 10
    responseTimeout      = ResponseTimeoutDefault
    requestVersion       = HTTP/1.1
    proxySecureMode      = ProxySecureWithConnect
  }
   (ConnectionFailure Network.Socket.getAddrInfo (called with preferred socket type/protocol: AddrInfo {addrFlags = [AI_ADDRCONFIG], addrFamily = AF_UNSPEC, addrSocketType = Stream, addrProtocol = 0, addrAddress = 0.0.0.0:0, addrCanonName = Nothing}, host name: Just "rformassspectrometry.github.io", service name: Just "443"): does not exist (nodename nor servname provided, or not known))
[WARNING] Could not fetch resource https://lgatto.github.io/QFeaturesScpWorkshop2021/articles/figs/SCP_framework.png: HttpExceptionRequest Request {
    host                 = "lgatto.github.io"
    port                 = 443
    secure               = True
    requestHeaders       = []
    path                 = "/QFeaturesScpWorkshop2021/articles/figs/SCP_framework.png"
    queryString          = ""
    method               = "GET"
    proxy                = Nothing
    rawBody              = False
    redirectCount        = 10
    responseTimeout      = ResponseTimeoutDefault
    requestVersion       = HTTP/1.1
    proxySecureMode      = ProxySecureWithConnect
  }
   (ConnectionFailure Network.Socket.getAddrInfo (called with preferred socket type/protocol: AddrInfo {addrFlags = [AI_ADDRCONFIG], addrFamily = AF_UNSPEC, addrSocketType = Stream, addrProtocol = 0, addrAddress = 0.0.0.0:0, addrCanonName = Nothing}, host name: Just "lgatto.github.io", service name: Just "443"): does not exist (nodename nor servname provided, or not known))
--- finished re-building ‘QFeatures_nutshell.Rmd’

--- re-building ‘advanced.Rmd’ using rmarkdown
--- finished re-building ‘advanced.Rmd’

--- re-building ‘read_scp.Rmd’ using rmarkdown
--- finished re-building ‘read_scp.Rmd’

--- re-building ‘reporting_missing_values.Rmd’ using rmarkdown

Quitting from reporting_missing_values.Rmd:56-60 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [bioconductor.org]:
TLS connect error: error:00000000:lib(0):func(0):reason(0)
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─scpdata::leduc2022()
 2.   └─ExperimentHub (local) leduc2022_pSCoPE()
 3.     └─ExperimentHub:::.get_ExperimentHub()
 4.       └─ExperimentHub::ExperimentHub()
 5.         └─AnnotationHub::.Hub(...)
 6.           └─base::tryCatch(...)
 7.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.                 └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'reporting_missing_values.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [bioconductor.org]:
TLS connect error: error:00000000:lib(0):func(0):reason(0)
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘reporting_missing_values.Rmd’

--- re-building ‘scp.Rmd’ using rmarkdown
--- finished re-building ‘scp.Rmd’

--- re-building ‘scp_data_modelling.Rmd’ using rmarkdown
Warning: ggrepel: 14 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘scp_data_modelling.Rmd’

SUMMARY: processing the following file failed:
  ‘reporting_missing_values.Rmd’

Error: Vignette re-building failed.
Execution halted