Comments (2)
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.
from rbioformats.
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...?
from rbioformats.
Related Issues (20)
- Install failure on Windows HOT 2
- Installation in R 4.0.0
- RBioFormats library needs internet connection to load HOT 5
- Slow to load when internet connection is on HOT 1
- Fails when downloads.openmicroscopy.org is down HOT 12
- Installation fails with slow internet, jar download times out
- Saving OIB: metadata is lost HOT 2
- Windows installation fails due to missing path HOT 5
- Create user cache directory if it doesn't exist HOT 1
- Error on install Linux R/4.2.0 HOT 2
- RBioFormats not working offline HOT 1
- Reading OME-Zarr (OME-NGFF) HOT 2
- `RBioFormats::coreMetadata(x)` does not work but `coreMetadata(x)` does HOT 3
- Package development depending on RBioFormats: How can I reliably set `java.parameters` when importing functions from RBioFormats into my package?
- Improve documentation of `read.image`
- Edit XML metadata
- initial values vs values after writing/reading are different HOT 1
- Null pointer exception the first time calling RBioFormats function HOT 1
- Load RBioFormats with an older version of bioformats? HOT 1
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from rbioformats.