pelkmanslab / iBRAIN_BRUTUS

A version of canonical iBRAIN (2015) deployed on BRUTUS cluster
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fuse_basic_data_v5 creates (misleading?) error #24

Closed tstoeger closed 7 years ago

tstoeger commented 9 years ago

according to log of fuse_basic_datav5 (FuseBasicData.*.results) there are several errors. Presently it is unclear to a user (like me), whether these errors are reasons for concerns or if the error messages indicate absence of a function, which has been deliberately removed from iBrain. On top, at least one of the errors appears to be related to a discontinued support of a certain functionality for newer versions of MATLAB running without java virtual machine (-nojvm)

10 plates gathered Saving /BIOL/sonas/biol_uzh_pelkmans_s7/Data/Users/RNAFish/IndividualExperiments/150819f-CytooChipsResub/BASICDATA.mat **\ CREATING ADVANCEDDATA

err1 =

   message: [1x80 char]
identifier: 'MATLAB:UndefinedFunction'
     stack: [2x1 struct]

*\ creating and saving ADVANCEDDATA failed on /BIOL/sonas/biol_uzh_pelkmans_s7/Data/Users/RNAFish/IndividualExperiments/150819f-CytooChipsResub.

Undefined function 'Detect_Outlier_levels' for input arguments of type 'double'. **\ CREATING ADVANCEDDATA2

err1 =

   message: [1x84 char]
identifier: 'MATLAB:UndefinedFunction'
     stack: [1x1 struct]

*\ creating and saving ADVANCEDDATA2 failed on /BIOL/sonas/biol_uzh_pelkmans_s7/Data/Users/RNAFish/IndividualExperiments/150819f-CytooChipsResub.

Undefined function 'Create_ADVANCEDDATA2_iBRAIN' for input arguments of type 'char'. ** CREATING BASICDATA.csv Convert_BASICDATA_to_csv: stored /BIOL/sonas/biol_uzh_pelkmans_s7/Data/Users/RNAFish/IndividualExperiments/150819f-CytooChipsResub/BASICDATA_150819f-CytooChipsResub.csv ** CREATING ADVANCEDDATA_html.csv

err1 =

   message: [1x89 char]
identifier: 'MATLAB:UndefinedFunction'
     stack: [1x1 struct]

*\ creating and saving ADVANCEDDATA_html.csv failed on /BIOL/sonas/biol_uzh_pelkmans_s7/Data/Users/RNAFish/IndividualExperiments/150819f-CytooChipsResub.

Undefined function 'Convert_ADVANCEDDATA_to_csv_HTML' for input arguments of type 'char'. **\ CREATING ADVANCEDDATA2.csv

err1 =

   message: [1x97 char]
identifier: 'MATLAB:UndefinedFunction'
     stack: [1x1 struct]

*\ creating and saving ADVANCEDDATA.csv failed on /BIOL/sonas/biol_uzh_pelkmans_s7/Data/Users/RNAFish/IndividualExperiments/150819f-CytooChipsResub.

Undefined function 'Convert_ADVANCEDDATA2_to_full_csv_iBRAIN' for input arguments of type 'char'.

{Error using figure This functionality is no longer supported under the -nojvm startup option. For more information, see "Changes to -nojvm Startup Option" in the MATLAB Release Notes. To view the release note in your system browser, run web('http://www.mathworks.com/help/matlab/release-notes.html#btsurqv-6', '-browser').

Error in check_dg_plate_correlations (line 86) figure() }

tstoeger commented 7 years ago

Closing some GitHub issues of mine which have been idle for around two years. Underlying issues might still be present.