Operation timed out after 300192 milliseconds with 0 out of 0 bytes received

[lwaldron]

I'm seeing this locally on wallabe4 in Docker, haven't tested yet on the Cloud. Do you see this too, @lgeistlinger @shbrief @LiNk-NY?

Quitting from lines 835-847 (Geistlinger_CNVWorkshop.Rmd)
  Error: processing vignette 'Geistlinger_CNVWorkshop.Rmd' failed with diagnostics:
  Operation timed out after 300192 milliseconds with 0 out of 0 bytes received
  --- failed re-building ‘Geistlinger_CNVWorkshop.Rmd’

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

  Error: Vignette re-building failed.
  Execution halted
Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted

[lgeistlinger]

which container are you using? bioc2020 or devel?

[lwaldron]

I'm using this latest as of this morning (there isn't a ludwigg/cnvworkshop:bioc2020 tag). Seems to be a download problem at ftp.ncbi.nlm.nih.gov, I suppose not much you can do about it:

lwaldron@wallabe4:~$ docker pull ludwigg/cnvworkshop:latest
latest: Pulling from ludwigg/cnvworkshop
Digest: sha256:73a259d1b1ff1daf428332cbe5ef35345060d9c980bf8e08d61840bd191172e7
Status: Image is up to date for ludwigg/cnvworkshop:latest
docker.io/ludwigg/cnvworkshop:latest
lwaldron@wallabe4:~$ docker run -it ludwigg/cnvworkshop:latest R -e "devtools::build_vignettes()"

Quitting from lines 847-859 (Geistlinger_CNVWorkshop.Rmd) 
Error: processing vignette 'Geistlinger_CNVWorkshop.Rmd' failed with diagnostics:
cannot open the connection to 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_report.txt'
--- failed re-building ‘Geistlinger_CNVWorkshop.Rmd’