Closed liudanmai11 closed 3 weeks ago
Hi, I think this error may be due to the multiple cores used in gbm, Please reinstall and retry using following code to see if it can run
res= ML.Dev.Prog.Sig(train_data = list_train_vali_Data$Dataset1,
list_train_vali_Data = list_train_vali_Data,
unicox.filter.for.candi = T,
unicox_p_cutoff = 0.05,
candidate_genes = genelist,
mode = 'single',
single_ml = "GBM",
nodesize =5,seed = 5201314,
cores_for_parallel=1)
Thank for your reply.However, the 'ML.Dev.Prog.Sig' function has no 'cores_for_parallel' parameters. And after I reinstalled the gbm package, I still got the same error.
---the number of the raw candidate genes is 35 --- ---the number of the common feature is 35 --- --- Data preprocessing --- [1] "Starting the data preprocess" [1] "Rejecting a null value" [1] "Gets the intersection of genelist and expression profile" [1] "Processing the input representation matrix" [1] "Data preprocessing completed" [1] "Stating the univariable cox regression" 6% 11% 17% 23% 29% 34% 40% 46% 51% 57% 63% 69% 74% 80% 86% 91% 97% [1] "Finished the univariable cox regression" ---the number of the final unicox filtered candidate genes is 6 --- [1] "CAPS" "BTBD16" "EFNA3" "VWA1" "WFDC10A" "AC117386.2" --- Start GBM --- terminate called after throwing an instance of 'std::length_error' what(): vector::_M_default_append Error in unserialize(node$con) : error reading from connection terminate called after throwing an instance of 'std::length_error' what(): vector::_M_default_append
Thank for your reply.However, the 'ML.Dev.Prog.Sig' function has no 'cores_for_parallel' parameters. And after I reinstalled the gbm package, I still got the same error.
---the number of the raw candidate genes is 35 --- ---the number of the common feature is 35 --- --- Data preprocessing --- [1] "Starting the data preprocess" [1] "Rejecting a null value" [1] "Gets the intersection of genelist and expression profile" [1] "Processing the input representation matrix" [1] "Data preprocessing completed" [1] "Stating the univariable cox regression" 6% 11% 17% 23% 29% 34% 40% 46% 51% 57% 63% 69% 74% 80% 86% 91% 97% [1] "Finished the univariable cox regression" ---the number of the final unicox filtered candidate genes is 6 --- [1] "CAPS" "BTBD16" "EFNA3" "VWA1" "WFDC10A" "AC117386.2" --- Start GBM --- terminate called after throwing an instance of 'std::length_error' what(): vector::_M_default_append Error in unserialize(node$con) : error reading from connection terminate called after throwing an instance of 'std::length_error' what(): vector::_M_default_append
Please reinstall Mime not gbm and we have add parameter "cores_for_parallel" before.
Hi, when I use ML.Dev.Prog.Sig function I get the following error, how can I solve this problem? Error in unserialize(node$con) : error reading from connection