Comments (6)
Sorry to hear that. I searched around. This seems a difficult problem without a final solution yet.
rstudio/rstudio#6692
I do not have Mac, thus, cannot test. If you find any solution, I am willing to revise iCAMP.
If you are using Rstudio, did you try the original R?
If R 4.x does not work anyway, you may have to install an old version of R (>=3.5) to run iCAMP, until R or the 'parallel' package developers find the solution.
If your dataset is not very large, you may use our galaxy pipeline http://ieg3.rccc.ou.edu:8080/. please email me ([email protected]) to set up your account.
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I believe I have found a temporary fix:
cl <- parallel::makeCluster(10, setup_timeout = 0.5)
Then specify nworkers= cl and it seemed to work for me. For others having this issue, try some of the other solutions on the above link if this doesn't work.
Thanks!
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Great. I will try to add this to the functions.
from icamp1.
The following code has been added to iCAMP (version >= 1.4.3, can be found in /RPckage/AllVersion).
paste0("RC",taxo.metric," i")
Example output files
c1<-try(parallel::makeCluster(nworker,type="PSOCK"))
if(class(c1)[1]=='try-error'){c1 <- parallel::makeCluster(nworker, setup_timeout = 0.5)}
if(class(c1)[1]=='try-error'){c1 <- parallel::makeCluster(nworker, setup_strategy = "sequential")}
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@bholt20 please let me know if the new version (1.4.3) can solve your problem. I will close this issue if no more question : )
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Yes, this fixed it. Thanks!
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Related Issues (20)
- Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent HOT 11
- Error in com.bin[[i]]: attempt to select less than one element in integerOneIndex HOT 8
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- ITS data? HOT 4
- Error in CreateFileBackedBigMatrix(as.character(backingfile), as.character(backingpath), : Problem creating filebacked matrix. HOT 2
- abundance weighted bMNTD & bNTI HOT 2
- OpenBLAS blas_thread_init: pthread_create failed for thread in betaMPD calculation HOT 4
- core, rare and other taxa HOT 2
- Error occured while runwhile bNRI.bin.big HOT 5
- Mismatch in values between vegdist Bray distances and RC.pc CB.obs HOT 2
- Some questions about OTUs in each group HOT 2
- Out of memory? HOT 7
- Error in oldname[j, 1:2] : subscript out of bounds HOT 5
- unsolved problem HOT 5
- an issue in bNTI.big.r HOT 1
- Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: subscript out of bounds HOT 5
- Results of bin.size.limit parameters to12 and 72 were same HOT 12
- Error in h(simpleError(msg, call)) : when running icamp.big HOT 2
- Solution to large dataset? HOT 3
- Error while computing bNRI for strict bins HOT 3
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