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rietho / IPO

A Tool for automated Optimization of XCMS Parameters
http://bioconductor.org/packages/IPO/
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MakeCluster(nSlaves, type = "PSOCK") #29

Closed tobigithub closed 8 years ago

tobigithub commented 8 years ago

Hi, under WINDOWS7 I uninstalled Rmpi and only use snow now. IPO fires up, but after the first optimization round it breaks. BTW this was a tested and working version. Central Carbon Metabolism was the script I used. SO first round is OK and then in the second DoE round it breaks, I guess everything is fine in the first round, then in the second round something happens.

Why would IPO built use makeCluster(nSlaves, type = "PSOCK") in the second round, but not in the first round? 

starting new DoE with:
min_peakwidth:  c(12, 28)       max_peakwidth:  c(35, 65)       ppm:    c(17, 32)       mzdiff: c(-0.001, 0.01) snthresh:       10      noise:  0       prefilter:      3       value_of_prefilter:     100     mzCenterFun:    wMean   integrate:      1       fitgauss:       FALSE   verbose.columns:        FALSE   nSlaves:        1       

 Starting snow cluster with 32 local sockets.
Detecting features in file # 1 : 1_QC.mzXML 
Detecting features in file # 2 : 2_QC.mzXML 
Detecting features in file # 3 : 3_QC.mzXML 
Detecting features in file # 4 : 4_QC.mzXML 
Detecting features in file # 5 : 5_QC.mzXML 
Detecting features in file # 6 : 6_QC.mzXML 

starting new DoE with:
min_peakwidth:  c(4, 20)        max_peakwidth:  c(35, 59)       ppm:    c(9.5, 24.5)    mzdiff: c(0.00175, 0.01275)     snthresh:       10      noise:  0       prefilter:      3       value_of_prefilter:     100     mzCenterFun:    wMean   integrate:      1       fitgauss:       FALSE   verbose.columns:        FALSE   nSlaves:        1       
Error in makeCluster(nSlaves, type = "PSOCK") : unknown cluster type
In addition: Warning messages:
1: package ‘Rcpp’ was built under R version 3.1.3 
2: In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.3)
than is installed on your system (0.12.0). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc mailing list at 
http://www.bioconductor.org/help/mailing-list. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
3: package ‘rsm’ was built under R version 3.1.3 
4: package ‘igraph’ was built under R version 3.1.3 
5: replacing previous import by ‘igraph::groups’ when loading ‘CAMERA’ 
Timing stopped at: 6.26 1.25 546.46 
>

T

tobigithub commented 8 years ago

Duplicate