Installation stuck at step "testing if installed package can be loaded from temporary location"

[QuinceyLv]

Hi,
I tried to install RBioFormats on R4.3.0:

BiocManager::install("aoles/RBioFormats")

── R CMD build ─────────────────────────────────────────────────────────────────

• checking for file ‘/tmp/9771460.1.SC1.q/RtmptHlfNa/remotes5b886ec82ce9/aoles-RBioFormats-5ec5fad/DESCRIPTION’ ... OK

• preparing ‘RBioFormats’:

• checking DESCRIPTION meta-information ... OK

• checking for LF line-endings in source and make files and shell scripts

• checking for empty or unneeded directories

• building ‘RBioFormats_0.99.14.tar.gz’

• installing source package ‘RBioFormats’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location

and the installation stuck at this step. How could I solve this? Thanks in advance.

[lambdamoses]

It seems that it's trying to download Bio-Formats at this stage, which can take a while depending on your internet, and I got

Warning in utils::download.file(bf_url, bf_jar, mode = "wb", quiet = FALSE) :
  downloaded length 0 != reported length 0
Warning in utils::download.file(bf_url, bf_jar, mode = "wb", quiet = FALSE) :
  URL 'https://downloads.openmicroscopy.org/bio-formats/6.12.0/artifacts/bioformats_package.jar': Timeout of 100 seconds was reached
Error: package or namespace load failed for ‘RBioFormats’:
 .onLoad failed in loadNamespace() for 'RBioFormats', details:
  call: NULL
  error: Failed to download Bio-Formats Java library.
  Check your internet connection and try again. Consider setting the environment variable R_DEFAULT_INTERNET_TIMEOUT to a value higher than 100.
Error: loading failed
Execution halted

Setting Sys.setenv(R_DEFAULT_INTERNET_TIMEOUT = 2000) solved the problem for me. Maybe use a larger value if your internet is slower.

[QuinceyLv]

It seems that it's trying to download Bio-Formats at this stage, which can take a while depending on your internet, and I got

Warning in utils::download.file(bf_url, bf_jar, mode = "wb", quiet = FALSE) :
  downloaded length 0 != reported length 0
Warning in utils::download.file(bf_url, bf_jar, mode = "wb", quiet = FALSE) :
  URL 'https://downloads.openmicroscopy.org/bio-formats/6.12.0/artifacts/bioformats_package.jar': Timeout of 100 seconds was reached
Error: package or namespace load failed for ‘RBioFormats’:
 .onLoad failed in loadNamespace() for 'RBioFormats', details:
  call: NULL
  error: Failed to download Bio-Formats Java library.
  Check your internet connection and try again. Consider setting the environment variable R_DEFAULT_INTERNET_TIMEOUT to a value higher than 100.
Error: loading failed
Execution halted

Setting Sys.setenv(R_DEFAULT_INTERNET_TIMEOUT = 2000) solved the problem for me. Maybe use a larger value if your internet is slower.

Thanks for reply. I had checked zzz.R and found:

if ( !file.exists(bf_jar) ) {
    # The default for timing out the file download is 60s
    # Temporarily increase it if this is the case
    orig_timeout <- getOption("timeout")
    options(timeout = max(100, orig_timeout))
    tryCatch(utils::download.file(bf_url, bf_jar, mode = "wb", quiet = FALSE),
             error = function(e) {
               file.remove(bf_jar)
               stop(
                 "Failed to download Bio-Formats Java library.\n  Check your internet connection and try again. Consider setting the environment variable R_DEFAULT_INTERNET_TIMEOUT to a value higher than 100.",
                 call.=FALSE)
             },
    finally=options(timeout = orig_timeout)
    )
  }
}

I tried to change the timeout or to download the jar package manually and change the "download.file" to "file.copy" from local, but either worked. Maybe Sys.setenv(R_DEFAULT_INTERNET_TIMEOUT = 2000) could save me...?