Fix affymetrix "Timeout was reached: Connection timed out after 10001 milliseconds"

[arkid15r]

Context

In order to restore staging/prod deploy process CI/CD tests need to be fixed.

Problem or idea

#14 176.6 installing to /usr/local/lib/R/site-library/xml2/libs
#14 176.6 ** R
#14 176.6 ** inst
#14 176.6 ** preparing package for lazy loading
#14 176.6 ** help
#14 176.7 *** installing help indices
#14 176.8 ** building package indices
#14 176.8 ** installing vignettes
#14 176.8 ** testing if installed package can be loaded
#14 177.0 * DONE (xml2)
#14 177.0
#14 177.0 The downloaded source packages are in
#14 177.0       ‘/tmp/RtmpVWxhtW/downloaded_packages’
#14 177.5 Bioconductor version '3.6' is out-of-date; BiocManager does not support R
#14 177.5   version '3.4.4'. For older installations of Bioconductor, use
#14 177.5   'source("https://bioconductor.org/biocLite.R")' and refer to the
#14 177.5   'BiocInstaller' vignette on the Bioconductor website
#14 177.5 Loading required package: usethis
#14 178.1
#14 178.1 Attaching package: ‘devtools’
#14 178.1
#14 178.1 The following object is masked from ‘package:BiocManager’:
#14 178.1
#14 178.1     install
#14 178.1
#14 178.2 'getOption("repos")' replaces Bioconductor standard repositories, see
#14 178.2 'help("repositories", package = "BiocManager")' for details.
#14 178.2 Replacement repositories:
#14 178.2     CRAN: https://cloud.r-project.org
#14 182.7 Bioconductor version 3.6 (BiocManager 1.30.20), R 3.4.4 (2018-03-15)
#14 182.7 Installing package(s) 'BiocVersion'
#14 184.4 Old packages: 'backports', 'BH', 'bit', 'bit64', 'bitops', 'blob', 'brew',
#14 184.4   'clipr', 'commonmark', 'covr', 'crayon', 'crosstalk', 'curl', 'DBI',
#14 184.4   'digest', 'dplyr', 'DT', 'evaluate', 'fansi', 'ff', 'git2r', 'highr', 'hms',
#14 184.4   'htmlwidgets', 'jsonlite', 'knitr', 'later', 'magrittr', 'markdown', 'mime',
#14 184.4   'pkgconfig', 'prettyunits', 'promises', 'purrr', 'R6', 'RCurl', 'renv',
#14 184.4   'rex', 'rprojroot', 'RSQLite', 'rstudioapi', 'stringi', 'sys', 'tidyr',
#14 184.4   'utf8', 'whisker', 'xfun', 'XML', 'xtable', 'yaml', 'boot', 'class',
#14 184.4   'codetools', 'KernSmooth', 'lattice', 'MASS', 'nnet', 'rpart', 'spatial'
#14 184.4 Warning message:
#14 184.4 package ‘BiocVersion’ is not available (for R version 3.4.4)
#14 194.4 Error in open.connection(x, "rb") :
#14 194.4   Timeout was reached: Connection timed out after 10001 milliseconds
#14 194.4 Calls: read_html -> read_html.default
#14 194.4 Execution halted
#14 ERROR: process "/bin/bash -o pipefail -c Rscript install_ensg_pkgs.R" did not complete successfully: exit code: 1
------
 > [ 7/15] RUN Rscript install_ensg_pkgs.R:
#14 184.4   'pkgconfig', 'prettyunits', 'promises', 'purrr', 'R6', 'RCurl', 'renv',
#14 184.4   'rex', 'rprojroot', 'RSQLite', 'rstudioapi', 'stringi', 'sys', 'tidyr',
#14 184.4   'utf8', 'whisker', 'xfun', 'XML', 'xtable', 'yaml', 'boot', 'class',
#14 184.4   'codetools', 'KernSmooth', 'lattice', 'MASS', 'nnet', 'rpart', 'spatial'
#14 184.4 Warning message:
#14 184.4 package ‘BiocVersion’ is not available (for R version 3.4.4)
#14 194.4 Error in open.connection(x, "rb") :
#14 194.4   Timeout was reached: Connection timed out after 10001 milliseconds
#14 194.4 Calls: read_html -> read_html.default
#14 194.4 Execution halted
------
Dockerfile.affymetrix:13
--------------------
  11 |
  12 |     COPY workers/R/dependencies/affymetrix/install_ensg_pkgs.R .
  13 | >>> RUN Rscript install_ensg_pkgs.R
  14 |
  15 |     COPY workers/data_refinery_workers/processors/requirements.txt .
--------------------
ERROR: failed to solve: process "/bin/bash -o pipefail -c Rscript install_ensg_pkgs.R" did not complete successfully: exit code: 1

Solution or next step

Troubleshoot and fix the timeout exception.

[arkid15r]

Apparently, the remote docker builder machine IP address was blocked. Resolved by moving to a new machine with different IP address.