Can't read in data on local host

[rachel662]

hi there, I can't seem to read in the pancreas image dataset upon following the instructions and i'm not sure why, it just seems to not be able to download the dataset from the URL. Would anyone be able to help me fix this problem? the error I get is shown below.

Error in download.file(url.cells, destfile = "data/PancreasData/CellSubset.zip") : download from 'https://data.mendeley.com/public-files/datasets/cydmwsfztj/files/f1e3b8dc-56be-4172-bbc4-3a6f9de97563/file_downloaded' failed In addition: Warning messages: 1: In download.file(url.cells, destfile = "data/PancreasData/CellSubset.zip") : downloaded length 277910408 != reported length 302347503 2: In download.file(url.cells, destfile = "data/PancreasData/CellSubset.zip") : URL 'https://md-datasets-public-files-prod.s3.eu-west-1.amazonaws.com/eb047fd4-e4b9-4c92-9f12-4c7c292ddd69': Timeout of 60 seconds was reached

best, Rachel

[nilseling]

Hi Rachel,

hmm, that's strange. I just tested the code on my side and it works fine. Could you please type the url https://data.mendeley.com/public-files/datasets/cydmwsfztj/files/f1e3b8dc-56be-4172-bbc4-3a6f9de97563/file_downloaded into your browser and see if you can manually download the cells? It could be that there was a temporary issue with Mendeleys server or an instable internet connection.

Cheers,

Nils

[rachel662]

Hi Nils, thanks for your help and for sharing the analysis scripts, if I manually download all the data I can read it in and use my own Rstudio. However it doesn't seem to work through the local host?

thanks again Rachel

[nilseling]

Hey Rachel,

are you using the docker container? I usually compiled the scripts inside the container on a linux server. But I also tested the container locally on my Mac now and I can download the data inside the container. However, it seems to be slightly slower than downloading it outside the container - so there could be a time-out kicking in if your internet connection is not stable. In any case, the analysis should be reproducible if you install the current Bioconductor release 3.12 on R 4.0 and open the cytomapper_publication R project.
Best,

Nils

[rachel662]

Hi Nils, yes, on the docker container I clicked Inspect, and then the last thing on that menu is Port, which has the local host you say to open that you can then open in your browser, I think perhaps it is the time-out that may be affecting things

I have the current Bioconductor release installed, and R version 4.0.3, if i type in the command BiocManager::install("cytomapper_publication")

I get this error `Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10) Installing package(s) 'cytomapper_publication' Warning message: package ‘cytomapper_publication’ is not available for this version of R

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages`

I don't know if there is another way to navigate to the cytomapper_publication R project?

thanks again for your patience, I am fairly new to coding and dealing with IMC data so really appreciate the help

Kind regards Rachel

[nilseling]

Hey,

using BiocManager::install you can only install packages. I was talking about the cytomapper_publication.Rproj file. First, clone the repository; Second, in RStudio, simply navigate to the cytomapper_publication.Rproj file in the Files tab on the lower right hand side and click on the file. This will open the cytomapper_publication project and set the working directory for you. In that way you can work locally and with a stable internet connection you should be able to download the files. Best,

Nils

[rachel662]

Hey Nils, thanks so much, I've now cloned the repository and will see if that works!

Best Rachel

[nilseling]

I assume that this is resolved now and will close the issue.