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COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
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constant Version Info: Could not resolve upgrade information in the alotted time. #277

Open antonkulaga opened 6 years ago

antonkulaga commented 6 years ago

Whenever I run any command with latest official docker image of salmon, as an example:

docker run combinelab/salmon:latest salmon swim

I get

Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
antonkulaga commented 6 years ago

Looks like --no-version-check does the job of avoiding this warning, however, make it is better to just make a command for version check instead of forcing users to do --no-version-check all the time to silence this error?

brendanwee commented 5 years ago

I am getting the same error on the latest binary distro. I am running CentOS Linux 7 (Core). Does this affect the performance?

micans commented 5 years ago

I got this error and was surprised to find the cause. I've added --no-version-check now, but I agree the default of phone-home behaviour is not great.

thoelken commented 5 years ago

I was trying to troubleshoot the contemplation period of salmon with monitoring utilities and just stumbled upon this issue upon submitting my own. The failed version check gets buried by the spew of warnings for too short/long transcripts for hg38 mrna.fna in my case.

The current behaviour is particularly irritating as I assumed, that salmon index -h just runs into a loop accidentally. The check takes multiple minutes to timeout. I am behind a proxy.

Please remove the version check by default, as this is not common behaviour of command line tools or anticipated by the user. Or at least please add a verbose message before checking "Checking for upgrades online...".