Error when Testing the pipeline

[Mirable8me]

Good afternoon! I want to use nichenet with OmniPathR. Please help me solve this problem: nichenet_test()

 Computing y column(s) for design. Not provided.
Mapping in parallel: mode = multicore; level = mlrMBO.feval; cpus = 4; elements = 16.
Error in stopWithJobErrorMessages(inds, vcapply(result.list[inds], as.character)) : 
  Errors occurred in 1 slave jobs, displaying at most 10 of them:

00006: Error in if (sd(prediction_vector) == 0) warning("all target gene probability score predictions have same value") : 
  missing value where TRUE/FALSE needed

[deeenes]

Hello, We're discussing in our group how can we support this pipeline. It's quite difficult to find out what's going on in the backend packages that the NicheNet pipeline uses. Meanwhile, I'd suggest to try to run it a few times, as several steps are non-deterministic, and randomly fail. If you keep getting the error, maybe a trace could be helpful to see at least where this error happens (traceback(), rlang::last_error(), rlang::last_trace()).

[Mirable8me]

.

Hello, We're discussing in our group how can we support this pipeline. It's quite difficult to find out what's going on in the backend packages that the NicheNet pipeline uses. Meanwhile, I'd suggest to try to run it a few times, as several steps are non-deterministic, and randomly fail. If you keep getting the error, maybe a trace could be helpful to see at least where this error happens (traceback(), rlang::last_error(), rlang::last_trace()).

Thanks for your reply! I restarted the function three times and it worked! However, now I am getting an error with the following function nichenet_networks()

[2023-10-19 16:10:43] [SUCCESS] [OmnipathR] Building NicheNet network knowledge
[2023-10-19 16:10:43] [SUCCESS] [OmnipathR] Starting to build NicheNet signaling network
[2023-10-19 16:10:46] [SUCCESS] [OmnipathR] Loaded 79722 interactions from cache.
[2023-10-19 16:10:49] [SUCCESS] [OmnipathR] Harmonizome (maayanlab.cloud): loaded 6013 records from cache
[2023-10-19 16:10:49] [SUCCESS] [OmnipathR] Harmonizome (maayanlab.cloud): loaded 12161 records from cache
[2023-10-19 16:10:49] [SUCCESS] [OmnipathR] Harmonizome (maayanlab.cloud): loaded 819 records from cache
[2023-10-19 16:10:50] [WARN]    [OmnipathR] HTTP 403
[2023-10-19 16:10:50] [WARN]    [OmnipathR] Failed to download `https://www.science.org/action/downloadSupplement?doi=10.1126%2Fscisignal.2001699&file=4_rs8_tables_s1_s2_and_s6.zip` (attempt 1/3); error: HTTP 403
[2023-10-19 16:10:55] [WARN]    [OmnipathR] HTTP 403
[2023-10-19 16:10:55] [WARN]    [OmnipathR] Failed to download `https://www.science.org/action/downloadSupplement?doi=10.1126%2Fscisignal.2001699&file=4_rs8_tables_s1_s2_and_s6.zip` (attempt 2/3); error: HTTP 403
[2023-10-19 16:11:00] [WARN]    [OmnipathR] HTTP 403
[2023-10-19 16:11:00] [ERROR]   [OmnipathR] Failed to download `https://www.science.org/action/downloadSupplement?doi=10.1126%2Fscisignal.2001699&file=4_rs8_tables_s1_s2_and_s6.zip` (attempt 3/3); error: HTTP 403
Error in `map2()`:
ℹ In index: 1.
ℹ With name: signaling_network.
Caused by error in `map2()`:
ℹ In index: 4.
ℹ With name: vinayagam.
Caused by error:
! HTTP 403

This problem is not resolved by restarting the function. Could you help with this?

[deeenes]

Oops, it's the same issue as #76. The Science journal makes it more and more difficult to download supplementary tables. But this one I can fix soon, here in OmnipathR.