Comments (6)
Hi @tobiasko,
Given that rocker/r2u
is currently (and will likely remain) fixed on the AMD64 system architecture, I encountered significant slowness in my Docker container since I'm running it on an ARM64 host system. Consequently, I decided to completely rebuild my container using debian:bookworm
as the base image and installing only the necessary components for my specific use-case, including rawrr
.
In this updated environment, buildRawrrExe()
successfully completed its task on the first attempt. This leads me to suspect that there may have been issues with the Rosetta translation from AMD64 to ARM64, causing the previous build to fail. I intend to upload the Dockerfile
on GitHub and will provide a link to it in this thread to ensure others can access a functional Docker container with rawrr
. If there's interest, I can adapt the Dockerfile to include only the essential requirements for running rawrr
as a contribution to this project.
from rawrr.
Hi @SamThilmany,
I am unfortunately not to familiar with building docker containers. Does the location /root/.cache/R/rawrr/rawrrassembly/
exist for the file system of the docker container? Can you place a file there using the command line of the container (is it writeable)? Have you tested the basic functionality of the mono compiler? Was is correctly build/installed in the container? On which platform do you run the docker container (OS)?
Have you ever tried to install rawrr in a bioc docker container?
https://www.bioconductor.org/help/docker/
Does it show the same behaviour?
Sorry for the many question.
Best,
Tobi
from rawrr.
The mono project homepage shows some basic tests for the mono compiler
https://www.mono-project.com/docs/getting-started/mono-basics/
from rawrr.
I think it would be nice to develop a recipe for rawrr
application within containers.
from rawrr.
Maybe it would even make sense to publish your docker image on docker hub? A container image based on Debian Bookworm might be interesting for people that don't like the bioconductor containers for some reason.
from rawrr.
The bioc containers incl. stuff like RStudio server, which is of course a cool thing for people that depend on an IDE, but there is for sure also people how prefer a stripped down minimal image.
https://github.com/Bioconductor/bioconductor_docker
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Related Issues (20)
- Get information on gradient HOT 1
- Enhancement - Complete readIndex() function HOT 9
- Peak charges for MS1 spectras HOT 4
- Spectrum scan centroid mZ, intensity and noises values do not match HOT 2
- Error in Example: Length of "x" and "y" are not matching HOT 3
- Read noise value for profile mode mass spectra HOT 4
- Read_Spectrum - Sum Spectra
- unit should be minute / auc computation in seconds HOT 24
- validate_rawrrSpectrum 'StartTime' HOT 4
- "Error: line 1 did not have 9 elements" for readIndex() and readChromatogram() + "Error : No scan vector is provided"for readSpectrum HOT 9
- Problem executing readChromatogram inside Singularity container HOT 5
- Add a check if `input` file exists and is not empty
- Error in if (rvs != "No RAW file specified!") { : the condition has length > 1 HOT 16
- Switch to RawFileReader 5.0.93 HOT 2
- different total number of Spectra in msconvert, compomics/ThermoRawFileParser and thermofisherlsms/RawFileReader HOT 2
- Request for auc.rawrrChromatogram HOT 3
- profile mode in readSpectrum HOT 11
- speed up readIndex/readSpectrum by base::textConnection HOT 14
- auc.rawrrChromatogram question
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