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/ , and they also have OS X binaries: 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
Tim On Sun, May 27, 2018 at 3:32 PM, Marta Moreno <[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]> 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]> > Date: Sunday, May 27, 2018 at 3:22 PM > To: "[email protected]" <[email protected]> > Cc: Matt Glasser <[email protected]>, HCP Users < > [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] 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]> 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]> > 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]> wrote: > > Perhaps you are running out of memory. > > Peace, > > Matt. > > From: <[email protected]> on behalf of Marta Moreno < > [email protected]> > Date: Saturday, May 26, 2018 at 1:50 PM > To: HCP Users <[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] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > ------------------------------------------------------------ > --------------- > Stephen M. Smith, Professor of Biomedical Engineering > Head of Analysis, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [email protected] http://www.fmrib.ox.ac.uk/~steve > ------------------------------------------------------------ > --------------- > > Stop the cultural destruction of Tibet <http://smithinks.net/> > > > > > > > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
