Thanks. I can install randomForest_4.6-14 instead. IS there any specific reason for needing version 4.6-12 to run hip_fix?
******************************************* Leah Moreno, PhD Associate Research Scientist Division of Experimental Therapeutics Department of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (914) 218-7311 email: [email protected] email: [email protected] > On May 30, 2018, at 7:52 PM, Timothy Coalson <[email protected]> wrote: > > That is the same line I used to install randomForest in a docker container. > I would guess that those look like assembly directives. Based on that, I > would guess that either randomForest uses some assembly code, and it doesn't > support the OS X compiler you are using, or that you somehow have a broken > compiler setup (less likely). > > The main possibilities I see: > > 1) do your processing using linux instead of OS X (VM, container, or a native > install) > 2) try installing gcc and gfortran on OS X, and getting R to use them to > build packages (probably messy, may need to rebuild R itself, we haven't > tested it) > > Tim > > > On Wed, May 30, 2018 at 8:59 AM, Marta Moreno <[email protected] > <mailto:[email protected]>> wrote: > Dear Tim, > > How did you install randomForest' version 4.6.12? I am getting the following > error (see below). Do I need R-devel as well to install randomForest? Please > advice this should be the last step before having hcp_fix running properly. > > install_version("randomForest", version = "4.6-12", repos = > "http://cran.us.r-project.org <http://cran.us.r-project.org/>”) > > (…) > > /var/tmp//ccP5LbYW.s:2671:2: error: unknown directive > .stabn 224,0,0,LBE141 > ^ > /var/tmp//ccP5LbYW.s:2673:9: error: unsupported directive '.stabs' > .stabs "",36,0,0,Lscope8-LFBB8 > ^ > /var/tmp//ccP5LbYW.s:2697:9: error: unsupported directive '.stabs' > .stabs "",100,0,0,Letext0 > ^ > /var/tmp//ccP5LbYW.s:2835:11: warning: section "__textcoal_nt" is deprecated > .section __TEXT,__textcoal_nt,coalesced,pure_instructions > ^ ~~~~~~~~~~~~~ > /var/tmp//ccP5LbYW.s:2835:11: note: change section name to "__text" > .section __TEXT,__textcoal_nt,coalesced,pure_instructions > ^ ~~~~~~~~~~~~~ > make: *** [rfsub.o] Error 1 > ERROR: compilation failed for package ‘randomForest’ > * removing > ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/randomForest’ > Installation failed: Command failed (1) > > Thanks a lot! > > -L > > ******************************************* > Leah Moreno, PhD > Associate Research Scientist > Division of Experimental Therapeutics > Department of Psychiatry > Columbia University Medical Center > 1051 Riverside Drive, Unit 21 > <https://maps.google.com/?q=1051+Riverside+Drive,+Unit+21+New+York,+NY+10032&entry=gmail&source=g> > New York, NY 10032 > <https://maps.google.com/?q=1051+Riverside+Drive,+Unit+21+New+York,+NY+10032&entry=gmail&source=g> > phone: (914) 218-7311 > email: [email protected] <mailto:[email protected]> > email: [email protected] <mailto:[email protected]> > >> On May 27, 2018, at 11:20 PM, Marta Moreno <[email protected] >> <mailto:[email protected]>> wrote: >> >> Thanks, Tim! I followed your advice and I am almost there… How did you >> install randomForest' version 4.6.12? I am getting the following error: >> >> install_version("randomForest", version = "4.6-12", repos = >> "http://cran.us.r-project.org <http://cran.us.r-project.org/>”) >> >> (…) >> >> /var/tmp//ccP5LbYW.s:2671:2: error: unknown directive >> .stabn 224,0,0,LBE141 >> ^ >> /var/tmp//ccP5LbYW.s:2673:9: error: unsupported directive '.stabs' >> .stabs "",36,0,0,Lscope8-LFBB8 >> ^ >> /var/tmp//ccP5LbYW.s:2697:9: error: unsupported directive '.stabs' >> .stabs "",100,0,0,Letext0 >> ^ >> /var/tmp//ccP5LbYW.s:2835:11: warning: section "__textcoal_nt" is deprecated >> .section __TEXT,__textcoal_nt,coalesced,pure_instructions >> ^ ~~~~~~~~~~~~~ >> /var/tmp//ccP5LbYW.s:2835:11: note: change section name to "__text" >> .section __TEXT,__textcoal_nt,coalesced,pure_instructions >> ^ ~~~~~~~~~~~~~ >> make: *** [rfsub.o] Error 1 >> ERROR: compilation failed for package ‘randomForest’ >> * removing >> ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/randomForest’ >> Installation failed: Command failed (1) >> >> Thanks! >> >> -L >> >>> On May 27, 2018, at 9:12 PM, Timothy Coalson <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> The way I solved this was to use the very latest R version (cran mirrors >>> contain debian and ubuntu packages, see >>> http://cran.wustl.edu/bin/linux/ubuntu/ >>> <http://cran.wustl.edu/bin/linux/ubuntu/> , and they also have OS X >>> binaries: http://cran.wustl.edu/bin/macosx/ >>> <http://cran.wustl.edu/bin/macosx/> ), then install devtools (this is the >>> main reason for installing the latest R, as getting devtools installed in >>> older R is an even bigger pain), and then use "install_version": >>> https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages >>> >>> <https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages> >>> >>> Tim >>> >>> >>> On Sun, May 27, 2018 at 3:32 PM, Marta Moreno <[email protected] >>> <mailto:[email protected]>> wrote: >>> I am using workbench v1.3. I have used R v3.3, R v3.4.and R v3.5. None of >>> them allowed me to install specified software packages versions required to >>> run hcp_fix: ('kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' >>> version 1.6.7 or 'randomForest' version 4.6.12), so I guess the error I am >>> getting now is regarding this issue. I have pasted the error below: >>> >>> Error in ctreefit(object = object, controls = controls, weights = weights, >>> : >>> no slot of name "remove_weights" for this object of class >>> "TreeGrowControl" >>> Calls: eval -> eval -> <Anonymous> -> ctreefit >>> Execution halted >>> >>> Please advice on which R version should I have installed to make it to >>> work. I have downloaded software packages and installing them in R as root >>> as follow: >>> > install.packages('/Users/alayar/Downloads/kernlab_0.9-24.tar', >>> > dependencies=TRUE) >>> Warning message: >>> package ‘/Users/alayar/Downloads/kernlab_0.9-24.tar’ is not available (for >>> R version 3.3.3) >>> >>> Thanks! >>> >>> -L >>> >>>> On May 27, 2018, at 4:24 PM, Glasser, Matthew <[email protected] >>>> <mailto:[email protected]>> wrote: >>>> >>>> There is no relationship between R and Workbench (or R and matlab). As to >>>> a Workbench/matlab incompatibility, we would need to know what version of >>>> Workbench and matlab to debug this. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: Marta Moreno <[email protected] >>>> <mailto:[email protected]>> >>>> Date: Sunday, May 27, 2018 at 3:22 PM >>>> To: "[email protected] <mailto:[email protected]>" >>>> <[email protected] <mailto:[email protected]>> >>>> Cc: Matt Glasser <[email protected] <mailto:[email protected]>>, HCP >>>> Users <[email protected] >>>> <mailto:[email protected]>> >>>> Subject: Re: [HCP-Users] error running hcp_fix >>>> >>>> Thanks, but with newer versions is not working either because R software >>>> packages such as 'kernlab' version 0.9.24, 'party' version 1.0.25, >>>> 'e1071' version 1.6.7 or 'randomForest' version 4.6.12, are incompatible >>>> with R 3.3 or 3.5. At least based on my experience. So could you please >>>> let me know which is the R version I need to install to have it compatible >>>> with workbench and also compatible with R software packages listed above >>>> that are needed to run hcp_fix? I am using a MAC pro, with workbench v1.3. >>>> >>>> This is becoming a nightmare so I would really appreciate your help. >>>> >>>> Thanks!, >>>> >>>> -L >>>> >>>>> On May 27, 2018, at 3:04 AM, [email protected] >>>>> <mailto:[email protected]> wrote: >>>>> >>>>> Hi - we've seen this in the past with specific combinations of matlab >>>>> version and workbench version. I'm not quite sure if the very latest >>>>> versions of both have the issue or not. >>>>> Cheers. >>>>> >>>>> >>>>>> On 27 May 2018, at 02:32, Marta Moreno <[email protected] >>>>>> <mailto:[email protected]>> wrote: >>>>>> >>>>>> I found the following error, please advice: (before is giving me some >>>>>> warnings about different functions that has same name as a Matlab >>>>>> builtin, I have pasted the output from last warning and first error). >>>>>> >>>>>> Which are the files that needs to be included in >>>>>> ‘CIFTIMatlabReaderWriter’ for the settings.sh? >>>>>> >>>>>> Warning: Function subsref has the same name as a MATLAB builtin. We >>>>>> suggest you >>>>>> rename the function to avoid a potential name conflict. >>>>>> > In path (line 109) >>>>>> In fix_3_clean (line 45) >>>>>> /bin/bash: /usr/local/workbench/bin_macosx64: is a directory >>>>>> Error using read_gifti_file_standalone (line 20) >>>>>> [GIFTI] Loading of XML file >>>>>> /private/var/folders/j2/__433pcd02l1cw9qkydkqs5h0000gn/T/tp6555679429695603.gii >>>>>> failed. >>>>>> >>>>>> Error in gifti (line 71) >>>>>> this = >>>>>> read_gifti_file_standalone(varargin{1},giftistruct); >>>>>> >>>>>> Error in ciftiopen (line 31) >>>>>> cifti = gifti([tmpfile '.gii']); >>>>>> >>>>>> Error in fix_3_clean (line 46) >>>>>> BO=ciftiopen('Atlas.dtseries.nii',WBC); >>>>>> >>>>>> Thanks! >>>>>> >>>>>> -L >>>>>> >>>>>> >>>>>>> On May 26, 2018, at 6:55 PM, Marta Moreno <[email protected] >>>>>>> <mailto:[email protected]>> wrote: >>>>>>> >>>>>>> You were right, now the problem is gone but still cannot find my >>>>>>> clean.dtseries >>>>>>> >>>>>>> Here is the output, I could not find any error in .ica folder: >>>>>>> hcp_fix RS_fMRI_1.nii.gz 2000 >>>>>>> processing FMRI file RS_fMRI_1 with highpass 2000 >>>>>>> running highpass >>>>>>> running MELODIC >>>>>>> running FIX >>>>>>> FIX Feature extraction for Melodic output directory: >>>>>>> RS_fMRI_1_hp2000.ica >>>>>>> create edge masks >>>>>>> run FAST >>>>>>> registration of standard space masks >>>>>>> extract features >>>>>>> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica >>>>>>> using training file: >>>>>>> /usr/local/fix1.065/training_files/HCP_hp2000.RData and threshold 10 >>>>>>> FIX Applying cleanup using cleanup file: >>>>>>> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion >>>>>>> cleanup set to 1 >>>>>>> >>>>>>> Please advice. >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> -L >>>>>>> >>>>>>> >>>>>>>> On May 26, 2018, at 2:52 PM, Glasser, Matthew <[email protected] >>>>>>>> <mailto:[email protected]>> wrote: >>>>>>>> >>>>>>>> Perhaps you are running out of memory. >>>>>>>> >>>>>>>> Peace, >>>>>>>> >>>>>>>> Matt. >>>>>>>> >>>>>>>> From: <[email protected] >>>>>>>> <mailto:[email protected]>> on behalf of Marta >>>>>>>> Moreno <[email protected] <mailto:[email protected]>> >>>>>>>> Date: Saturday, May 26, 2018 at 1:50 PM >>>>>>>> To: HCP Users <[email protected] >>>>>>>> <mailto:[email protected]>> >>>>>>>> Subject: [HCP-Users] error running hcp_fix >>>>>>>> >>>>>>>> Dear experts, >>>>>>>> >>>>>>>> I am getting the following error. Please advice: >>>>>>>> >>>>>>>> hcp_fix RS_fMRI_1.nii.gz 2000 >>>>>>>> processing FMRI file RS_fMRI_1 with highpass 2000 >>>>>>>> running highpass >>>>>>>> running MELODIC >>>>>>>> running FIX >>>>>>>> FIX Feature extraction for Melodic output directory: >>>>>>>> RS_fMRI_1_hp2000.ica >>>>>>>> create edge masks >>>>>>>> run FAST >>>>>>>> registration of standard space masks >>>>>>>> extract features >>>>>>>> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica >>>>>>>> using training file: >>>>>>>> /usr/local/fix1.065/training_files/HCP_hp2000.RData and threshold 10 >>>>>>>> FIX Applying cleanup using cleanup file: >>>>>>>> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion >>>>>>>> cleanup set to 1 >>>>>>>> sh: line 1: 10513 Killed: 9 >>>>>>>> /Applications/MATLAB_R2017b.app/bin/matlab -nojvm -nodisplay >>>>>>>> -nodesktop -nosplash -r "addpath('/usr/local/fix1.065'); >>>>>>>> addpath('/usr/local/fsl/etc/matlab'); fix_3_clean('.fix',0,1,2000)" >> >>>>>>>> .fix.log 2>&1 >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> -L >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> HCP-Users mailing list >>>>>>>> [email protected] <mailto:[email protected]> >>>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >>>>>>> _______________________________________________ >>>>>>> HCP-Users mailing list >>>>>>> [email protected] <mailto:[email protected]> >>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >>>>>> _______________________________________________ >>>>>> HCP-Users mailing list >>>>>> [email protected] <mailto:[email protected]> >>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >>>>> >>>>> --------------------------------------------------------------------------- >>>>> Stephen M. 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